If the crank wasn't checked for straightness and if it wasn't "normalized" after grinding it could be the trouble. Were the bearings that came out of the engine prior to the rebuild all evenly worn in the same amount?
Seems silly, but are the motor and transmission mounts all OK?
Pre-ignition (ping) at sub-audible levels can also cause a vigration from harmonics being set up in the crank. Are you flirting with large advance or compression? Are the carbs accurately balanced and adjusted (better a little rich than lean).
Hmmmm.
Are all your belt driven accessories in good condition?
Plasti-gauging journals is one of my little quirks as I will always do it if possible (doubles time of engine builds) so of course I recommend it.
The only other things rotating are the transmission and camshaft (OK, the dizzy and oil pump too).
Does vibration reduce/go away when the clutch is dis-engaged?
I suppose it is possible that a cam blank from an aftermarket producer could be off-center and introduce a vibration.
Wears me out!

Mike!