Sorry, I didn't quite understand all of this but I assume that this was intended to me??I'm with Nutter. You have not come back with the sync yet. Though, you do mention the vib goes away at higher rpm where it's spinning so fast why whip the throttle when it is either a bearing wobble is I doubt it on the long shot. It could be and now tell me what year is I am stuck with a year being is it carb or injector?
Shaft to shaft is have you at least inspected for valve adjust being it is strange/new to you and who/when/where are the service documents being how long it sat with clogged injector holes or a jet hardly feeding a cylinder that hesitates to the point it is a long shot the sync is or is not it is clear that valve adjust and sync is eliminate your mechanical vibrations. Then you can tell if a fat injector is spitting drops or mists is did you change plugs or check who is lean/sooty rich?
SYNC Done????? WOT say ye? One elimination at a time so you can know next time is stop chasing your tail is what is the compression of each cylinder, (after checking the valve lash).
That bike is hours from ready for your ass salt is FunINN wit day road.