You may have an air leak (extra air getting in) between the carbs & the engine. Inlet manifold rubbers do crack on Hondas but Yamahas are the worst.
Check for cracks, check the o rings (each end of inlet manifold) & check for leaks from air-box to carbs
Carbs need to be balanced (synchronised) to let the engine run smoothly but will not produce those symptoms if left unbalanced.
You should also check the HT leads & spark plug caps for shorting, run the bike in the dark & look for sparks going to earth (sometimes you can only hear a ticking as the spark jumps across). Make sure the leads are not touching anything during this procedure
Ride safe
Bike-Doc
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