Ive noticed that kind of feeling when the oil starts to break down, but havent had any problems at all shifting, still solid and positive, when i was using the honda hp oil 10-40 after roughly 2k miles or so, it would get slightly "clunkier" and shifted a little harder than I'd prefer,
I switched to the Repsol 10-50 fully syn and im just guessing that the fully syn with the higher tolerance for heat, and resisting breakdown at higher temperatures is what did it. havent had any of the hard shifting, or "clunk" with that oil. another thing ive noticed is that honda trannies seem to be slightly harsher it he shifting process than some other bikes.
as far as too thick, once the engine and oil and all the goods are running hot, shouldn't be too much of a problem, don't race bikes use a thicker weight oil, as they are running hotter?