What the $

I’m not sure how much I’ve spent on the 68 Mustang coupe and probably shouldn’t look. I purchased this car in the fall of 2016 and went nuts! Took the 6 out and replaced it with a 347 Stroker, subframe connectors, 9 in rear end, a whole new drivetrain. It was sweet, but now I have a Tremec 6 speed transmission in it. I now have a vibration and I can’t find where it’s coming from. I have balanced the drive shaft 3 times check pinion angles changed tires. It seems to be in the transmission. We pulled it apart and it seems fine. Any ideas out there?
 
Just to be clear, with a different trans and the new engine it was smooth?
Vibe came instantly with the trans swap?
You replaced, trans, flywheel, clutch, and driveshaft and that is all?
 
I saw no mention of U-joint replacement.

Information about when and how you hear/feel these vibrations could help. ON the throttle/off, with engine speed, with vehicle speed... etc.