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?
--nothing looked unusual to me or a real machanic.
Seems silly, but are the motor and transmission mounts all OK?
--all new
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).
--switching new carbs made no difference and running them rich enough to start in cold weather without a choke (as rich as you can get without stalling) made no difference.
It is an E head and was bored to 2.2 liters compression is high but never calculated it out. It has the stock coil with pointless electronic distributer.

Hmmmm.
Are all your belt driven accessories in good condition?
--spose i could take off the belt and rev it up to see if it goes away, would be a good first try as it is easy.

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). --new distributer and oil pump. ..
Does vibration reduce/go away when the clutch is dis-engaged?
--it appears to be related to rpm's with or without gears engaged.
I suppose it is possible that a cam blank from an aftermarket producer could be off-center and introduce a vibration.
Is it possible that the timing gear could be off? new timing stock not steel,and crank gear installed with engine.