Transmission, drive shaft and differential question

You started off correct in removing and checking the shaft

Have you tried reving the engine to simulate cruise speed, both in neutral with clutch engaged (foot off the pedal) and with clutch depressed? Might be engine/ belt/ accessory such as alternator

at what road speed does this occur? Is it possible, EG, that due to rear axle ratio and small tires, you are simply running on the highway at overly high engine RPM?

Also consider that sometimes something simple like an exhaust pipe rattling against some part of the vehicle can SEEM like a vibration, when it is only "that."

I assume you vigorously wiggled the pinion at the rear axle to feel for play in the bearings.

Also I had a strange vibration, with a swapped For 9" in my 67 Dart. In the end, it turned out that one of the differential side gears (spiders) had worn out the differential case in which it rides, and so the inboard (splined) end of the axle and the bearing were sloppy in there.