Pinion Angle/Tailshaft Bushing

Did you indicate the bellhouse, before slaming the tranny in? that is to say; can you say with surety that the crank and the tranny are on the same centerline?
A)Still there when in neutral gliding, B)but reduced.C)Can feel roughness when pushing clutch in at that speed.D)It is noticed in the float zone of the throttle while cruising only and from the trans forward.E)Can feel it in the shifter and F)even a bit in the steering wheel.
This says you have multiple issues; 4 or 5 by my count.and possibly a 6th.
A) Still there Could mean some of it is after flywheel
B)Reduced vibration with the engine now idling, could mean that some of the vibration is in the engine.
C)Could be in the bellhouse
D)could be in the rods or wristpins or the tune.
E) Something is going on inside the tranny, or at it's tailshaft
F) if you feel it in the steering wheel this rarely has anything to do with the powertrain. The most likely is a blown cord in a front tire, followed by out of balance wheels, then too much toe-in, and lack of caster.

g) Sometimes these all conspire to set the body itself into an oscillation of it's own. It typically happens at 55 to 62 in our A-bodies.

I once had your problem pretty much exactly as you describe. I about tore my hair out looking for it. I spent huge blocks of time searching for it. In the end, I pulled the 4.30s out and swapped in 3.55s. This made it bearable.
The engine,flywheel and clutch were dead smooth. It was there with an indicated and checked for parallelism bellhouse,with multiple trannys, and two balances of the D/S. lt did not go away with pinion angle adjustments. Nor by removing the wheels, drums,axles,or by swapping out the chunks. I concluded it was the body.
It is still there today.