If mcintirf spins the inner shaft with no blades attached and gets a wobble or vibration the it comes down to the shaft of the flybar. And the flybar is SOOOoooo fussy that he can probably count on that being off a little. Oddly, I had a flybar that was perfectly straight but the end weights didn't match - and of course I had vibration.
So I'll throw this in as a thought after your ideas.
Spin the inner shaft. If there is vibration, pull the flybar and spin just the shaft. Watch the head closely for any wobble.
Check that upper bearing and cup also. I've had a problem with the bearing not seating and that can really mess things up.

Have fun with your search for the vibration. If you have to, pull both shafts and roll them on a glass plate or counter top or equivalent. You'll find it. And anything bent can be straightened if you are patient.

Soloboss