Buy at least 1 step larger pilot.
In my experience raising the main jet needle to richen the mid range simply caused flooding at low rpms. I suggested it as a temporary fix, but this may be causing your excessive richness on one side. Currently I actually dropped my needle 1 notch below stock (leaner) and my idle, very low rpms, and starting are reliable. I have pods in addition to exhaust and with 3 steps up on the main jet I am still way too lean in the mid and high range.
In my experience the carbs on these bikes do
not respond well to tuning with the main jet needle. I, and another user, have had to lower the main jet needles and step way up on mains to compensate for this leaning action.
Check out this thread for my attempt at an explanation for this phenomenon:
http://www.xs400.com/forum/showthread.php?t=5338
I just ordered every main jet size from 147.5 to 160, but they won't come in until next week.
If your main jet needles are allowing fuel to flood into the venturi the idle mix will be impossible to determine; you'll get false rich readings from the plugs and might lean your idle air mix when in fact it is too lean. At one point I exhaustively started the bike, only let it idle for two minutes (no revving at all), and then pulled the plugs, adjusted, and repeated until the plugs look yellowish, but before they begin to be carbon fouled.
Be extra super careful removing the plugs a lot. I already had to sleeve one side of my engine. Also if you're removing the plugs a lot take off the points cover. This reduces the risk of cross threading on the left side. Only finger tighten the plugs to start.