Codes (any code) won't make the ECM work differently (the problem that caused the code not-withstanding), and clearing them does nothing but re-set the counters.
The AMC code wouldn't cause a vibration. IMO, safe to ignore it.
I only mentioned 'in your head' because more than one of us has got back on a Buell after an extended time off one and thought WOW this vibrates a lot! Especially as they free decel. I can't think of anything else to check that would cause a vibration besides the things mentioned already. Timing wouldn't change, you say it still runs fast so I'd
assume you'd know if you had a dead cylinder. They'll go 70 mph fairly easily on one cylinder
Run it and make sure both head pipes at the head are hot? IR temp gun or spray a little water.
I didn't re-read the whole thread, can you get in the ECM to see AFV or EGO correction? Both should be close to 100, no need to be exact, close is fine.