engine/trans vibration

I have a bad cyclical vibration coming from my 65 barracuda engine/trans that I cannot identify. the vibration is felt through the whole chassis. The vibration starts only after the engine/trans is warm/driven for a few miles, no vibration when cold.
Some background, I have a 92 360 magum crate engine with a 65 904 trans. i just had the 904 professionally rebuilt for street strip, after reinstalling the trans I noticed the vibration at around 45-50 MPH. Immediately I thought something wrong with the trans, most likely the rebuilt converter (this was the same converter that was in the car before vibration, just rebuilt). I pulled trans, sent just the converter back to the trans guy, he said there was nothing wrong, but I insisted he install mopar performance weights as recommended for the magum eng.
I reinstalled converter and trans...still same vibration. I thought maybe other drivetrain issue: drives shaft/tire/rear end etc. so I put car up on jack stands, disconnected drive shaft, so just the engine and trans was isolated and take the rest of the drive train out of the equation. I still have the vibration, the engine has a slight constant vibration through the whole rpm range but the real annoying cyclical vibration (it rises and falls) is at 15-1800 RPM. You feel it in the seat/steering wheel/gas pedal.
Any one have any thoughts what to look for??