Author Topic: Yamaha XJ600S Seca II - Problems  (Read 19622 times)

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Offline bzr

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Yamaha XJ600S Seca II - Problems
« on: September 08, 2008, 06:44:02 pm »
So I just bought a 1997 Yammy Seca II with 18,000 miles to learn how to ride on while I finish my CB550F project (pics coming soon, I swear). Paid 1200 for it (including helmet) and took it for a spin that afternoon.

Of course, in my typical "ambitious but rubbish" style, I took it up a hill and ran out of talent. I ended up stalling it 5 or 6 times.  :-\ And on the 7th time, it wouldn't start up again - it turned over barely, but just made a clicking sound. I ended up having to push that thing back to my house over a mile, which is pretty embarrassing in broad daylight.

Anyway, it won't start up now at all, the headlight lights up but it makes a clicking sound from under the seat. I tried to jump start it today but to no avail. The hill I killed it on is pretty far from where I can bump start it. So I'm assuming it's a problem with the starter that the  >:( PO didn't mention...

I have a friend's father coming by on Sunday to take a look at it. Afterwards I'm gonna call a local MC shop and hope they make house calls. Think you can beat both of those to the chase with some advice?

/fail
1976 Honda CB550F

Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #1 on: September 08, 2008, 10:29:35 pm »
Oh, and...I'm starting the bike in neutral, holding down the clutch, and every time I thumb the starter button the oil light turns on. I can't see the correlation here but maybe you guys can.  ???
1976 Honda CB550F

Offline Shenanigans

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Re: Yamaha XJ600S Seca II - Problems
« Reply #2 on: September 08, 2008, 11:08:18 pm »
Whats the voltage at the battery?
   This pretty much sums it up.   76' CB592 cafe. 69 750 project, 03 CBR954, 75 750 super sport.

Offline edbikerii

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Re: Yamaha XJ600S Seca II - Problems
« Reply #3 on: September 09, 2008, 05:42:16 am »
Classic symptoms of dead battery.  I had a 97 myself (I bought it new), and those bikes are absolutely bulletproof.  I put well over 30K miles on mine without a single problem (other than crash repairs).  Nice purchase.
SOHC4 #289
1977 CB550K - SOLD
1997 YAMAHA XJ600S - SOLD
1986 GL1200I - SOLD
2004 BMW R1150R

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Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #4 on: September 09, 2008, 03:14:52 pm »
If that's the case, then anybody in the Syracuse area want to come by and help a brother out?  ;D

(No, really...please? Shoot me a PM, I'm free all week/weekend.)
1976 Honda CB550F

Offline Shenanigans

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Re: Yamaha XJ600S Seca II - Problems
« Reply #5 on: September 09, 2008, 04:34:14 pm »
I happen to be in syracuse for a bit. PM me and I will come help you out the best I can.
   This pretty much sums it up.   76' CB592 cafe. 69 750 project, 03 CBR954, 75 750 super sport.

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Re: Yamaha XJ600S Seca II - Problems
« Reply #6 on: September 11, 2008, 01:38:56 pm »
So you ever get the charger?
   This pretty much sums it up.   76' CB592 cafe. 69 750 project, 03 CBR954, 75 750 super sport.

Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #7 on: September 11, 2008, 10:34:57 pm »
It's shipped already, going to arrive tomorrow. I'll try it out tomorrow and let you know how it works out.
1976 Honda CB550F

Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #8 on: September 16, 2008, 06:47:19 pm »
So I finished charging the battery with my new (waterproof!) Battery Tender, and nothing blew up in my face or scalded my eyeballs out. Tried to start it up again. It turned over and started...but when I gave it some throttle it died instantly. I tried it again and I had to hold the start button down after it turned over, but had to keep it held while the engine was half-idling, half-still trying to get a spark, apparently. So, dead battery, and I'll have to shell out some cash and a ride to the nearest Advance Auto Parts for a new one...unless you guys think it's something else.

God, I hope it's not the starter...
1976 Honda CB550F

Offline Shenanigans

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Re: Yamaha XJ600S Seca II - Problems
« Reply #9 on: September 16, 2008, 07:00:12 pm »
Since the health of the battery is proportioned to how well it can turn over the starter. Its probably the battery. That bike, unless the PO abused it, is not very likely to have starter problems. It looked in good shape to me.
   This pretty much sums it up.   76' CB592 cafe. 69 750 project, 03 CBR954, 75 750 super sport.

Offline edbikerii

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Re: Yamaha XJ600S Seca II - Problems
« Reply #10 on: September 16, 2008, 07:01:11 pm »
How old is the battery?  If you don't know for sure, then yeah, just replace it.  I got the AGM type for not too much at Pep Boys.
Doesn't sound like the starter, since it turned over and started!

Sorry if this is a dumb question, but are you using the choke?  Also, this bike has a vacuum activated petcock, so it won't run unless there is sufficient engine vacuum to the petcock to keep the fuel flowing.  Try putting the petcock in the "prime" position (IIRC) for a bit before you start it up to make sure you are getting enough gas.  Once running, return it to the normal position (RUN?).

Maybe another dumb question, but are you sure there is enough gas in the tank?  When I was a total newbie, I watched the previous owner pour some gas into the tank and start the bike.  I made the deal, and then went to get plates for the bike.  When I got back and tried starting the bike, it cranked but wouldn't start.  I tried and tried, but nothing.  Turns out that the jerk PO had drained the gas back out after the deal was done and I had left.

Sorry if these questions seem silly, but some newbies to bikes just don't know these things.  I know that when I bought my CB550 all those many years ago, I really didn't know how to operate a choke or a petcock, and then when I bought my Seca II, the vacuum petcock was totally different.

So I finished charging the battery with my new (waterproof!) Battery Tender, and nothing blew up in my face or scalded my eyeballs out. Tried to start it up again. It turned over and started...but when I gave it some throttle it died instantly. I tried it again and I had to hold the start button down after it turned over, but had to keep it held while the engine was half-idling, half-still trying to get a spark, apparently. So, dead battery, and I'll have to shell out some cash and a ride to the nearest Advance Auto Parts for a new one...unless you guys think it's something else.

God, I hope it's not the starter...
SOHC4 #289
1977 CB550K - SOLD
1997 YAMAHA XJ600S - SOLD
1986 GL1200I - SOLD
2004 BMW R1150R

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Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #11 on: September 17, 2008, 05:44:16 pm »
Sorry if this is a dumb question, but are you using the choke?  Also, this bike has a vacuum activated petcock, so it won't run unless there is sufficient engine vacuum to the petcock to keep the fuel flowing.  Try putting the petcock in the "prime" position (IIRC) for a bit before you start it up to make sure you are getting enough gas.  Once running, return it to the normal position (RUN?).

I filled the tank last week, thought about that too. Today I tried it with the petcock in all three positions, still nothing.

I'll see if I can bum a ride to the nearest Advance Auto Parts for a maintenance-free YTX9-BS.  :-[
1976 Honda CB550F

Offline Sporkfly

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Re: Yamaha XJ600S Seca II - Problems
« Reply #12 on: September 18, 2008, 06:39:57 pm »
It really sounds like the battery. Let us know how that goes!

PS: Pics?!  ;D
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Offline edbikerii

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Re: Yamaha XJ600S Seca II - Problems
« Reply #13 on: September 18, 2008, 08:16:14 pm »
I don't know how you are so patient!!!  I would have been to the shop imediately!  I'm excited to hear that you got that bike running!

Sorry if this is a dumb question, but are you using the choke?  Also, this bike has a vacuum activated petcock, so it won't run unless there is sufficient engine vacuum to the petcock to keep the fuel flowing.  Try putting the petcock in the "prime" position (IIRC) for a bit before you start it up to make sure you are getting enough gas.  Once running, return it to the normal position (RUN?).

I filled the tank last week, thought about that too. Today I tried it with the petcock in all three positions, still nothing.

I'll see if I can bum a ride to the nearest Advance Auto Parts for a maintenance-free YTX9-BS.  :-[
SOHC4 #289
1977 CB550K - SOLD
1997 YAMAHA XJ600S - SOLD
1986 GL1200I - SOLD
2004 BMW R1150R

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Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #14 on: September 24, 2008, 06:12:32 pm »
So I walked the 3 miles to the nearest Advance Auto Parts, battery in hand, and bought a new one. It's a generic MF 12-volt sealed battery that was apparently made by some company called EPM and was the only one they had in stock. "Ready to install", it said on the side. So I installed it, fired it up again, and...nothing.

Same problem as before. Barely turns over, headlight lights up, etc. I played with the choke and petcock settings; when the latter is in the regular position and the choke is applied, the engine revs to 2500RPM and down again when I apply the throttle.

Any ideas, again? Oh, and pictures coming soon when I can find some time between classes.
1976 Honda CB550F

Offline edbikerii

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Re: Yamaha XJ600S Seca II - Problems
« Reply #15 on: September 25, 2008, 07:46:07 am »
Are you sure that that shop charged the battery up for you FULLY?  If a battery is used without an initial full charge, it can never utilize its full capacity, and its life is significantly reduced.  Find out whether they actually put it on a charger at the shop (probably not).

How long are you letting it warm up once started, before you start applying the throttle?  Let it run for a good five minutes.  If all is well, the idle, with the choke applied, should rise over a few minutes to about 4K RPM when it is fully warmed up.

Drain out any old gasoline in the tank, burn it up in something else, like your car.  Look for any debris in the old gas like rust flakes from the tank.  Buy a can of SeaFoam for the gas tank, follow the directions on the can using fresh gas.  I actually use it much stronger than the directions, but that's a risk I'm willing to take, and you may not be.  SeaFoam will take some time to loosen up any varnish (old gas) deposits in the carbs, and you may have to run a few treated tanks through to really get her to wake up.

So I walked the 3 miles to the nearest Advance Auto Parts, battery in hand, and bought a new one. It's a generic MF 12-volt sealed battery that was apparently made by some company called EPM and was the only one they had in stock. "Ready to install", it said on the side. So I installed it, fired it up again, and...nothing.

Same problem as before. Barely turns over, headlight lights up, etc. I played with the choke and petcock settings; when the latter is in the regular position and the choke is applied, the engine revs to 2500RPM and down again when I apply the throttle.

Any ideas, again? Oh, and pictures coming soon when I can find some time between classes.
SOHC4 #289
1977 CB550K - SOLD
1997 YAMAHA XJ600S - SOLD
1986 GL1200I - SOLD
2004 BMW R1150R

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Offline ColinMc

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Re: Yamaha XJ600S Seca II - Problems
« Reply #16 on: September 25, 2008, 08:17:36 am »
Even if it's "Ready To Use" you really should trickle charge any motorcycle battery overnight before using it. 2amp works fine. If you have a voltmeter check the voltage at the battery, I can almost promise it's below 12. Get that new battery nice and fully charged and then try again. If that still doesn't help then you need to track the problem.

Does the oil smell like gas?
1976 CB750K - Cafe Project...taking forever
1984 Honda MB-5 - MB-8 conversion in process
2001 Ducati 748 - Built 996 motor sleeper

Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #17 on: October 02, 2008, 01:37:07 pm »
Good news, everybody...IT WORKS!


Finally got around to sorting my bike out. Tried starting it in front of my friends, to no avail, and naturally they laughed about it. After they left, I realized that the kickstand was down and the kill switch wasn't letting it start. :bangin: So I took it off the stand, put the choke on, let it rev for a few minutes, turned off the choke, and took it around the block for an hour. And it's alive!

And I only stalled it twice.  ;D

Here it is in all of its glory:








Thanks for all of your help, especially Chris (Shenanigans) for going out of his way and coming over. If you don't mind I can post some pics here of your bike with mine. I've definitely appreciated it.
« Last Edit: October 02, 2008, 01:49:49 pm by bzr »
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Offline Shenanigans

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Re: Yamaha XJ600S Seca II - Problems
« Reply #18 on: October 02, 2008, 03:27:21 pm »
Glad to see it started, I would have never realized that a lot of bikes have a kickstand safety feature. I don't mind the pictures being posted at all, go for it. Now get riding! :)
   This pretty much sums it up.   76' CB592 cafe. 69 750 project, 03 CBR954, 75 750 super sport.

Offline edbikerii

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Re: Yamaha XJ600S Seca II - Problems
« Reply #19 on: October 02, 2008, 05:50:36 pm »
The kickstand safety switch should only stop the engine from running if the bike is in gear.  Seems like you need to figure something else out there.  You should be able to start and let the bike run on the sidestand as long as the trans is in neutral and the kill switch is in the "run" position.

Anyway, I'm glad to hear that you got it running one way or another.  I love those bikes, and still miss mine. 
SOHC4 #289
1977 CB550K - SOLD
1997 YAMAHA XJ600S - SOLD
1986 GL1200I - SOLD
2004 BMW R1150R

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Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #20 on: October 02, 2008, 06:47:21 pm »
The kickstand safety switch should only stop the engine from running if the bike is in gear.  Seems like you need to figure something else out there.  You should be able to start and let the bike run on the sidestand as long as the trans is in neutral and the kill switch is in the "run" position.
It was in first gear at the time, I forgot to mention.
1976 Honda CB550F

Offline edbikerii

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Re: Yamaha XJ600S Seca II - Problems
« Reply #21 on: October 02, 2008, 07:34:15 pm »
Then it is a good thing you've got that safety switch, or you'd be fixing some plastic right now!

The kickstand safety switch should only stop the engine from running if the bike is in gear.  Seems like you need to figure something else out there.  You should be able to start and let the bike run on the sidestand as long as the trans is in neutral and the kill switch is in the "run" position.
It was in first gear at the time, I forgot to mention.
SOHC4 #289
1977 CB550K - SOLD
1997 YAMAHA XJ600S - SOLD
1986 GL1200I - SOLD
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Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #22 on: October 09, 2008, 08:32:00 pm »
So I've been riding it for a few times now. (God, is it fun!) But I hate having to turn on the choke every time I start it up. It wasn't even that cold today, about 72 degrees out. Hell, there were people playing Frisbee shirtless.

Think I need a tuneup or something? Or something simple like adding more gas?
1976 Honda CB550F

Offline ColinMc

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Re: Yamaha XJ600S Seca II - Problems
« Reply #23 on: October 09, 2008, 09:19:59 pm »
Even in warmer weather, it's not odd to have to use the choke to start any bike if it's been sitting for a few hours or longer...varies from bike to bike. I know my FZ750 was pretty cold blooded like that, after sitting for more than an hour or two i'd have to use a little choke just to start it up. My 250 ninja is the same way...my cb750 doesn't run yet lol. My Norton only needs choke if it's been sitting overnight or longer, BMW same deal...
1976 CB750K - Cafe Project...taking forever
1984 Honda MB-5 - MB-8 conversion in process
2001 Ducati 748 - Built 996 motor sleeper

Offline edbikerii

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Re: Yamaha XJ600S Seca II - Problems
« Reply #24 on: October 09, 2008, 09:21:46 pm »
Well, it really shouldn't be such a burden to flip that handy little lever.

That bike does have a reputation for being "cold blooded" and requiring a few minutes to warm up.  However, you can fix it by drilling out the brass plugs on the carbs that cover the idle mixture screws and richening up the idle a bit.  I did that myself, and found it to be a nice improvement.  I think you've got to take off the tank, use a tiny drill bit, then screw in a small screw, then use a vise-grip on the screw and just pull the plugs out.  Don't bother putting them back when you are done adjusting.

On the other hand, it is pretty easy to screw that up and accidentally drill through a screw or something, so you might want to ride the bike for awhile and enjoy it before you start tinkering.  Just use the choke and enjoy.

So I've been riding it for a few times now. (God, is it fun!) But I hate having to turn on the choke every time I start it up. It wasn't even that cold today, about 72 degrees out. Hell, there were people playing Frisbee shirtless.

Think I need a tuneup or something? Or something simple like adding more gas?
SOHC4 #289
1977 CB550K - SOLD
1997 YAMAHA XJ600S - SOLD
1986 GL1200I - SOLD
2004 BMW R1150R

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Offline Buber

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Re: Yamaha XJ600S Seca II - Problems
« Reply #25 on: October 10, 2008, 12:32:45 am »
Check the fuel pump operation. My wife has this bike, and every time it stays longer than a week, you need to crank it a lot - it has to do with vacuum operated fuel pump.
Oh, hold on, you have choke lever on the handlebars? So you should have electric one..
Hmm, air and fuel filter to check? Iridium plugs would help too....
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Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #26 on: November 04, 2008, 10:00:32 pm »
Been riding it for a while, giving it the Italian tune-up it needs. Took it to redline a few times last week.

Dumb question, however: I removed the cracked turn signals from the front of the bike, and now it won't start. What am I missing here (besides the obvious signals)? I'm crap with electrics, can I still ride it while I wait for a new set of signals to come in?
1976 Honda CB550F

Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #27 on: December 08, 2008, 12:20:05 am »
Well #$%*, it's been a while since I read this thread. But I got something that will almost make this worth reading...;)

Turns out my cheap-assed Advance Auto Parts battery was as dead as Jimmy Hoffa. So I took it down to the store and wrangled a new one for free, from the one-year warranty. Sweet. Reinstalled the busted turn signals, and now it's parked for the winter in my friend's garage. Gonna pour some stabilizer I bought from a local Yamaha shop and fill the tank and tires.

Some pictures - for my photography project I managed to borrow a car suction kit from our school, and strapped it to the tank. I took some pictures at different speeds:




^ 8 second exposure.


^ I personally love this shot.



^ This one I got an A for because I photoshopped the needles in place. In reality, I was going less than 10mph. ;D
« Last Edit: December 08, 2008, 12:32:44 am by bzr »
1976 Honda CB550F

Offline edbikerii

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Re: Yamaha XJ600S Seca II - Problems
« Reply #28 on: December 08, 2008, 07:06:23 am »
Glad you got that bike on the road again!  I really miss mine.

You should photoshop the neutral light out, too.
SOHC4 #289
1977 CB550K - SOLD
1997 YAMAHA XJ600S - SOLD
1986 GL1200I - SOLD
2004 BMW R1150R

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Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #29 on: August 07, 2009, 02:52:47 pm »
I was hoping I wouldn't have to resurrect this thread. The Yammy's been riding fine ever since, until today...

Going down a hill, applied the brakes, downshifted twice, let go of the clutch too soon, it ended up stalling and when I tried to restart it I got nothing. Had to put it on full choke to get any sort of idle, at which point the revs climbed to 3500RPM. Taking it off the choke, even a little bit, killed off the idle. Even after putting it in gear when I let go of the clutch the bike stalled out again.

Fortunately I was only a few feet from my house because I ended up having to push it all the way home. images/smilies/wallbash.gif

The valves were ticking noisier than usual and there was this constant, repeating booming sound as well. Checked the battery and it still read normal voltage, so it may not be the ignition system.

Any ideas?

Oh, and an hour earlier when I was starting it up to go on my ride, it took an unusually long time for the bike to run on choke before it had a constant idle. And before that it sat for about a week.
1976 Honda CB550F

Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #30 on: August 18, 2009, 07:46:16 pm »
Quick update: just ran a compression test and got 115, 120, 115, 125. The battery still has 12 volts in it, and it sounds like only one or two cylinders are firing.

My friend suspects that I may need new plug wires, just like on the Honda...which means I'll have to drill them out of the coils (I'm planning NGK wire splices on the Honda for now). Any other possibilities as why it won't run smoothly?
1976 Honda CB550F

Offline edbikerii

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Re: Yamaha XJ600S Seca II - Problems
« Reply #31 on: August 18, 2009, 08:49:24 pm »
Have you checked for spark?  Disconnect spark plug wires one at a time.  Put a screwdriver in each of the plug wires, and hold it 1/4" from the cylinder head (hold the insulated end so you don't get shocked).  Crank the engine (make sure the kill switch is ON), and look for an arc to gap from the screwdriver to the cylinder head.

Bad wires, coil or ignition module will have no spark or a weak spark.

Which cylinders are not firing?  When it is running, spray some WD-40, or even just plain water on the exhaust pipes right up near the exhaust valves.  See which one(s) are not boiling off the water, and you will know which ones are not firing.  A failed coil will not fire on both of the cylinders that it is connected to.  I don't remember what cylinders each coil serves on the Seca II, but you should be able to just look at it and see which coil the plug wires connect to.

When you did the compression test, how did the plugs look?  Were any of them wet with gas or oil?  Any damage?

Don't forget, you need compression (yours seems fine to me), fuel, air and spark.
SOHC4 #289
1977 CB550K - SOLD
1997 YAMAHA XJ600S - SOLD
1986 GL1200I - SOLD
2004 BMW R1150R

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Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #32 on: August 24, 2009, 09:13:39 pm »
So the bike's been sitting for a week now, and testing it out it won't even crank over. The starter just kind of whimpers itself into oblivion (and that irritating buzzing noise).

Battery reads 12 volts, high beam, signals, and horn all still work. So I fear it's a bad starter. Do motorcycle shops make house calls?
1976 Honda CB550F

Offline edbikerii

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Re: Yamaha XJ600S Seca II - Problems
« Reply #33 on: August 25, 2009, 01:03:56 pm »
Battery is dead, try to charge it up and then get it load tested (free at most auto parts stores).

So the bike's been sitting for a week now, and testing it out it won't even crank over. The starter just kind of whimpers itself into oblivion (and that irritating buzzing noise).

Battery reads 12 volts, high beam, signals, and horn all still work. So I fear it's a bad starter. Do motorcycle shops make house calls?
SOHC4 #289
1977 CB550K - SOLD
1997 YAMAHA XJ600S - SOLD
1986 GL1200I - SOLD
2004 BMW R1150R

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Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #34 on: August 27, 2009, 08:27:15 pm »
Well, after a furious wrenching session tonight, I still have problems.

All 4 spark plugs show spark, so I'm definitely getting that to the engine. Cleaned out the airbox, realized that no fuel was getting past the petcock. So I cleaned that out too and reinstalled it, tried to jump start it from our Civic and...nothing. Battery is completely dead, and I fear that I may still not even have fuel flowing in the lines, they still felt kind of stiff.

When I had the battery load tested yesterday the guy at the battery shop recommended that I set it on a charger, which I did. Over 20 hours later (the battery tender manual recommends 15 hours) the battery was still dead. So the plan is to get the battery replaced under warranty, which may be tricky since I accidentally threw out the receipt.

After that...we'll see.
1976 Honda CB550F

Offline DavePhipps

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Re: Yamaha XJ600S Seca II - Problems
« Reply #35 on: September 01, 2009, 07:00:37 am »
I  would check the regulator/rectifier on the bike. From all the charging and jumpstarting your doing I  would say that it's toast, or at least getting there.
Get a multimeter and test the RR, and all relays
Some nice diagnostic instructions here
http://www.electrosport.com/technical-resources/diagnosis-center.php

BTW every time i've tried jump starting from anything I have had to replace the regulator/rectifier. The batteries are 8 amp on these bikes, if the electrical system gets hit with large amperage it seems to fry the RR. I  could be wrong, this is just  from personal experience.
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Offline edbikerii

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Re: Yamaha XJ600S Seca II - Problems
« Reply #36 on: September 01, 2009, 08:11:11 am »
It can't hurt to check the regulator/rectifier, but I have jump started my old XJ600S (electronic regulator/rectifier) and my CB550 (mechanical regulator/rectifier) several times over the years with no ill effects.  I have heard of people who have accidentally reversed the wire polarity when jumpstarting and blown electrical components, but I have never seen that happen from normal jumpstarting with booster cables done correctly.

I absolutely would AVOID jumpstarting if at all possible, however.  The best bet is to get yourself a good automotive battery charger that shuts off automatically (you'll need it for the rest of your life, anyway), set it at 2amps or less to charge, and charge up your battery fully.

In any event, the regulator/rectifier is not the cause of your running problems.

So, you know that you are getting spark, right?  You also know that you have good compression because you ran the compression test.  So what's left?

You also need fuel and air.

Check your air filter (yes, pull the tank, I'm afraid.  It really isn't that hard).  Maybe a mouse or a squirrel made a nest in there or something.

Check your fuel delivery.  Are the spark plugs wet when you pull them out after trying to start the engine unsuccessfully (with choke on, of course)?  Are all four of them wet?  Does the engine fire at all?

Could your petcock be clogged?  Could your carb jets be clogged?  You must put the petcock on the "Prime" position, since those bikes have a vacuum actuated petcock for safety reasons in the event of a tip-over.

Could the vacuum diaphragm in the petcock be cracked or leaky?  Connect a hose to it and see if it flows fuel when in Prime.  Try again while you apply vacuum to the vacuum line (a MityVac would be a great tool to own for this, too).  If you apply vacuum to the vacuum line (careful not to drink any fuel here - use a Mity-Vac if you can), does it hold the vacuum?

Could the fuel pump be defective?  Your bike has a vacuum driven fuel pump, too.  Apply vacuum to it and see what kind of flow you get.  This is a common failure mode, I understand.  I've seen that other owners have upgraded their fuel pumps to the electric fuel pumps available on later years (in Europe, at least).

So, first charge up that battery properly, and then get back into the game.  Don't give up.  I really love those bikes, and still regret the day I sold mine.

I  would check the regulator/rectifier on the bike. From all the charging and jumpstarting your doing I  would say that it's toast, or at least getting there.
Get a multimeter and test the RR, and all relays
Some nice diagnostic instructions here
http://www.electrosport.com/technical-resources/diagnosis-center.php

BTW every time i've tried jump starting from anything I have had to replace the regulator/rectifier. The batteries are 8 amp on these bikes, if the electrical system gets hit with large amperage it seems to fry the RR. I  could be wrong, this is just  from personal experience.
SOHC4 #289
1977 CB550K - SOLD
1997 YAMAHA XJ600S - SOLD
1986 GL1200I - SOLD
2004 BMW R1150R

Jetting: http://forums.sohc4.net/index.php?topic=20869.msg258435#msg258435
Needles:  http://forums.sohc4.net/index.php?topic=20869.msg253711#msg253711

Offline bzr

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Re: Yamaha XJ600S Seca II - Problems
« Reply #37 on: September 01, 2009, 12:52:17 pm »
I've already pulled the tank (which was surprisingly easy, only two bolts) and cleaned out, washed, and dried off the air filter. Is it ok to use WD-40 on an air filter, or will I have to shell out the whopping $3 or so dollars for K&N Air Filter Oil?

I've also cleaned out the petcock and reinstalled it. The spark plugs are getting spark and are dry. At the time, I didn't know if the engine was firing because the battery was completely toast. I'm at school now, but the battery has been charged overnight and is now sitting on my battery tender. I've also added more fuel to the tank in case it's something as stupid as I ran out of oil.

I'll probably be making a visit home on the weekend of the 18th so I can work on the bike more and see if it runs. And I'll definitely be checking all of those things you outlined, as well as getting my fairing fixed.
1976 Honda CB550F

Offline edbikerii

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Re: Yamaha XJ600S Seca II - Problems
« Reply #38 on: September 01, 2009, 01:11:59 pm »
If you are using a K&N, then shell out the $3 for filter oil.  The oil is what traps the dust.  WD40 won't trap anything.  Also, you're supposed to wash the filter with gasoline, I believe.  Did you follow K&N's instructions?

So, does the petcock flow fuel.  I know you've cleaned it, but did you check for fuel flow both on prime and when in Run position with vacuum applied?

For fixing fairings, go to Lowe's or Home Depot or a plumbing supply store and purchase ABS Cement (black).  This stuff is what the fairings were originally made of.  The solvent actually melts the original ABS plastic and effectively fuses it back together when you apply it sparingly.  Be very careful at first because it does dissolve the original plastic, and you don't want to apply too much.

If you are careful, you can apply the ABS cement to the rear of fairing cracks, and the repair can be as solid or more solid than the original part without needing to re-paint.

Please try this in an inconspicuous part of your fairing first so that you don't discover that your fairing is made of something else and I've given you bad advice, ok?

Once you are comfortable with this stuff, you can do all kinds of cool things with it!

I've already pulled the tank (which was surprisingly easy, only two bolts) and cleaned out, washed, and dried off the air filter. Is it ok to use WD-40 on an air filter, or will I have to shell out the whopping $3 or so dollars for K&N Air Filter Oil?

I've also cleaned out the petcock and reinstalled it. The spark plugs are getting spark and are dry. At the time, I didn't know if the engine was firing because the battery was completely toast. I'm at school now, but the battery has been charged overnight and is now sitting on my battery tender. I've also added more fuel to the tank in case it's something as stupid as I ran out of oil.

I'll probably be making a visit home on the weekend of the 18th so I can work on the bike more and see if it runs. And I'll definitely be checking all of those things you outlined, as well as getting my fairing fixed.
SOHC4 #289
1977 CB550K - SOLD
1997 YAMAHA XJ600S - SOLD
1986 GL1200I - SOLD
2004 BMW R1150R

Jetting: http://forums.sohc4.net/index.php?topic=20869.msg258435#msg258435
Needles:  http://forums.sohc4.net/index.php?topic=20869.msg253711#msg253711