as you rebuild, should needle depth be set in the middle of the five spaces on the shank, inspite of the changes to breathing and backpressure via the exaust and breather changes?
Set everything up according to the book, then ride the bike and adjust as necessary. Once you have those carbs back on the bike, you can change jets and change the needle position without having to remove the carbs. My feeling is that you don't know the true impact of any of the exhaust/airbox changes on YOUR bike. Do plug chop tests.
This is a procedure from
http://www.jpcycles.com/Tech/Articles/jettingpipes.aspxHere is a basic procedure to determine what jet to change. First, change the components such as pipes or air cleaner and get yourself 3 or 4 sets of new plugs, gapped and ready to install. We need to have access to the idle mixture screw, so we need to drill out the plug covering it. Once this is done, screw it in until it bottoms lightly, then back out 11/4 turns. Put a piece of masking tape around your throttle. Pick an easily seen reference point on your switch housing and mark on the tape where the zero (0) throttle position is. Open the throttle wide open, and mark on the tape the full throttle point. Half way between these marks mark again, and divide the 2-1/2's in 1/2 again. When you are though, you will have a mark at 0, 1/4, 1/2, 3/4 and Wide Open Throttle on the throttle sleeve.
Next, start the bike and warm it up so that it idles without the use of the enrichner. Once that's done, while wearing a set of mechanics gloves, remove the spark plugs and install a new set. Take the bike out and ride it for about 10 to 15 miles at 1/4 throttle if possible.
Things get a little complex now, so pay attention. We need to do what's called a "plug chop". This is where you pull the clutch, kill the ignition, and pull to the side of the road (carefully of course) WITHOUT ALLOWING THE BIKE TO IDLE. Still using your mechanic gloves, remove a plug and look at the color. If they are black and sooty, you are running rich on the pilot jet and need to reduce the amount of fuel by installing a smaller jet. If they are clean white, you are lean and need to give the engine more fuel by using a larger pilot or turn the mixture screw out a 1/4 turn. If they are brown no change is required. To aid in tuning, when you go in with the mixture screw, you get a leaner mixture. Out you richen the mixture. As a general rule of thumb the idle mixture should be 1-1/4 to 1-1/2 turns out when you have selected the right pilot jet. Repeat your test with fresh plugs for 1/2 throttle. Here in order to make a change, we can add fuel only with a stock needle by shimming with tiny washers under the needle. Every shim you add richens the midrange. The Dynojet tuner kits are equipped with a needle that has grooves in the end to adjust the position with a clip. Remember the higher on the needle the clip is the leaner the midrange becomes.
Install the appropriate jet you have decided upon (or make needle change), and a new set of plugs and redo the test. Repeat this until you have the correct light chocolate appearance.
The main jet is your cruising jet and needs to be tested above 3/4 throttle. It requires nice stretch of open road, or better yet a drag strip. Repeat the same type of test as before at 3/4 throttle and full throttle, doing your plug chop. Make changes accordingly. An additional test that is handy is to get up to, fourth gear at about 4000 RPM. Open the throttle all the way then immediately let off the throttle about 1/8. If the engine slows just a bit, the jet is close, if it seems to pick up speed or RPM; the main jet is too lean. If it hesitates or stumbles, the main is too rich. Change jets and test again.
After you have the jets close, I just ride about 50 to 75 miles observing the performance of the bike at different speeds. Poor acceleration, pinging, knocking, surging and popping or spitting through the carburetor suggests you're still lean. Black smoke, sooty exhaust, smell of unburned fuel and a rough idle suggest too rich. When I get back from the ride, I pull the plugs once more and see what I've got. If they are tan, light chocolate and the bike runs good, I'm done.