Is there any chance that the PO installed a high-compression piston (like a Wiseco)?    

The stock piston assembly weighs 507 grams.  The 94mm Wiseco weighs 455 grams.  That's a whopping 52 gram difference.  I currently have a 94mm Wiseco in mine and it shakes a bunch more than the stock piston.  It's tolerable, but I definitely prefer the stock vibration level.  My butt and hands are totally numb after an hour in the saddle at high speed.  You can do a quick check; test your compression. If its significantly more than 150 psi there's a good chance you have a high compression piston in there.

Is there any chance that the PO might have had the crankcase open and possibly got the counter-balancer shaft timing marks messed up?  The balancer shaft has to be timed to the crankshaft.  Only way to do that is with the crankcase split, the gears are inside.

Regarding engine mount bolts, don't forget the top mount.  There are three bolts that secure the cylinder head to the frame.

Good luck.  Let us know what you find.

I think you should find someone familiar with the bike and let someone else see this Horrible vibration,, They DO rattle a body a bit,,
What speeds are your gear changes?
Are you holding the grips tight?