Probably not the issue but when was the last time you adjusted your valves? If an exhaust valve is too tight it could cause a slight miss at idle and clear up at higher speeds. If this is the problem, don't drive the bike till the clearances are fixed otherwise you'll be looking at a valve job.
One other thing, did this problem show up right after pulling your carbs or some time after? Right after usually means the problem was self induced.
