Vibration Imbalance @3000rpm

Guys,
318 engine with upgrades heads, intake etc. When I had a 904 behind it there were no problems. When I switched to a 833 4 speed I am now getting balance issues.
1. I checked both and replaced one engine mount.
2. I had the driveshaft shortened and balanced by "the guru" in our area.
3. the imbalance is present in neutral

I'm guessing I have three things to consider;
1. the flywheel
2. the pressure plate and clutch
3. the transmission input shaft
Everything related to the transmission was bought used and I do not know their history.
My question to the experts is what would you consider first? What can I test?