Need help with vibration!!

If I had to guess, like they mentioned - the external banace on thef ront of the crank, with the internal balance on the rear, could be creating some harmonics as rpms rise. Normally the weight offsetting the imbalance is either within the main caps (internal and best way to balance) or outside the caps(external and the cheap way). That gives each end of the crank the same "input" in terms of vibrations and torsional load. I think your problem lies there. It's not enough during a free rev, but is enough when the crank is loaded. I'd also look into aligning the bellhousing to the new engine.

If you're in gear driving in 3rd (figure around 30-40mph) and creaping up towards 3500 - so it's shaking - and you press in the clutch without taking your foot off the gas pedal entirely, what happens to the vibration?