did you synchronize using a manometer??? if not, you can get one from JCWhitney that isn't too expensive, and very handy for any of these old bikes. its very easy to use...and it will definitely smooth out the idle if out of synch.
if you do a full tune up, start with adjusting the cam chain tension and valves before you check points and timing/ignition. if you make any carb adjustments, make sure you then check your timing and point gap as they may have been slightly altered from the carb changes. don't forget to check idle mixture settings, that will throw off a good idle as well.
my problem is that i want everything to be absolutely PERFECT, but keep in mind that an engine with 30 year old carbs and mechanical ignition is not going to idle or behalf like a fuel injected electronic ignition computer controlled engine. BUT I am constantly impressed by how good you can get these motors to run if kept properly in tune!!!
