welcome to the club and ur super close to me so we can combine forces and get everything working!!!
first thing with your brake..... get a speedbleeder and the speedbleeder IV bag to catch the brake fluid. also i had a similar issue with my whole brake system.
where is your hard line that goes to the caliper? i would highly recommend either pulling one form sportwheels or buying a new one. there is probably some crazy reason someone on the forums knows why the honda engineers decided to engineer a hard line into the caliper and not put the brake line straight into the brake caliper for some reason so i would recommend putting it back in. with the hard line it properly routes the brake line so if it decides to shift around it wont get caught in your tire or rim. your line is literally hanging/floating/flopping around :0
you might have to take apart you MC again. i had to seriously soak the MC in some gas and seafoam over night then take an assortment of carb cleaner wires. i notice that the really little hole in the MC was clogged. i also shot 2 cans of carb spray through it and compressed air to get everything out. also take a look at the actual MC cylinder if there is any heavy pitting on the inside. i notice that the MC piston thing you pulled out was pretty heavily caked with rust. how did the actual cylinder look?
i also run a SS line and a banjo switch for the brake like so we have the same setup.
also did you take apart your caliper? how is the piston and cylinder? how are the seals? its easy and cheap to rebuild the brake caliper so i would take it apart and put a new seal in it just in case. i mean when was the last time that was done? it wouldnt be very fun if that blows out
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adjusting the clutch is also very not fun. there are 3 points you have to adjust. First i usually start with the handle. i screw the adjuster all the way in and then back it out maybe a quarter of the way out. then a the clutch lever thing on the clutch case i back that screw all the way out until the line is tight. then i adjust the nut and screw on the bottom of the case rocking the bike back and forth and seeing when the clutch engages and disengages. its alot of fiddling and there is probably a better way of doing this and anyone correct me if im wrong im no expert.
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electrical wise i would ditch the stock fuse block. get a waterproof fuse block with automotive blade fuses. go through the wires methodically and get alot of electro contact spray and some fine sand paper. i went through all my connections cleaned them off with the sand paper to remove any corrosion or jumk and a good spritz of electro contract cleaner. then i take some dielectric grease grease and put the connector back on.
also go through the controls and blast it with electro contact spray or take it all apart like i did and really clean up the connections especially around the buttons and dab everything with the dielectric grease. its weird that there isnt any gasket or anything for the controls so the grease i feel is important to keep the moisture out.
i would also make sure the bike is properly grounded. there should be 2 grounds in the headlight bucket itself. the wires are green and they are actually connected to the bolt that holds the headlight bucket on the ears i dont see them in the pic. i would look at the main ground and even take down the paint so that the ground is straight on the frame. also clean the ground connector ends. this bike has a weak charging system and electrical stuff in general. i actually took the time to convert everything to LED and threw in a 35w HID kit to take the load off the alternator charging thing.
also i would check if your getting the proper charge. i read that the alternator thing dosnt really start charging until the bike is at a certain RPM. so if you just sputtering around the neighborhood then you might be draining the battery.
make sure your charging your battery on the lowest setting on your trickle charger also. maybe even remove the battery and tip it side to side to make sure you get the majority of those air bubbles out.
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also change out your chain. the bike can only use a standard heavy duty chain. it looks like your using an o ring or x ring or whatever chains they use on modern bikes. you can only use a standard heavy duty chain because the o ring chains are much wider and your chain is actually cutting into the side of you engine case by the front sprocket. take off your shifter and side cover and you will notice it.
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in regards to your carbs possibly being off sync ummm i have some sync gauges we can check that out with. about your pod filters.... i personally havent had any experience with them..... i feel like its kind of an xbox vs ps3 or microsoft vs apple. some people love them some people hate them. i never went the pod way because i just didnt need any more variables or stuff to fiddle with when building by bike for the first time.
ive read stories about how the bike will never be perfectly in sych because the stock bread box isnt used to stabilize the turbulence of the air when it gets sucked into the motor or you have to re jet or just a bunch of stuff. i think after 75 the bikes use a different tuned or style of carb to run the bikes more lean because of the EPA stuff. i know my 75 runs rich but after that year the bikes run a little more lean. so maybe your uni pod filters are messing with your sync. or there just straight up not synced right.
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also another awesome thing about these bikes is that i highly recommend using pure premium without any ethonal blended into the gas.
http://pure-gas.org/with the gas prices as expensive as it is 4.30 around my house the pure premium is extra uber expensive but it will help your bike out. so with the extra dollar a gallon for the pure premium with that fact that these bikes dont get stellar gas millage to begin with (or mine anyways or im trying to compare it to modern bikes) dont think your saving money lol.