they are bench synched though. is this dedfinately the problem with the idle?
Can't say definitely. But I have cured erratic idle return by vacuum synching carbs. Bench synching synchronizes carbs. Vacuum sync synchronizes the cylinders with variations they may have in breathing or compression across the cylinders.
I have no personal reason to go against spec, but i set the valves the way he suggested and the bike ran much better.
In theory, increasing the clearances reduces the lift and duration of the cam by some small amount. It makes sense if you are running the engine very hot and hard, as the metal's heat expansion likely takes up the added clearance. But, for a stock street bike, I'll stick with Honda specs., which I thought accounted for the a hot engine anyway. The clearances are set with engine cold. Certainly if the clearances are too large, the tappet smacks the valve stem rather than pushing on it. This can mushroom the stem or the adjuster face, making clearances ever larger. But, I don't know where "too large" is.
ONE MORE possible KINK:
the bike is A LOT noisier when the transmission is engaged. is this normal or do I have an issue with my tranny?
This may also be an artifact of unequal cylinder firing impulses due to vacuum synch issues. When the crankshaft changes speed, the trans gears alternate which tooth face is making contact. And, the trans "clacks" in time with the cylinder unevenness. Gear engagement alters the mass subjected to the rotational speed change and may intensify the emanated noise.
But, then, I can't hear your engine noise either. (Sound diminishes with the square of the distance.

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Cheers,