Definately sounds like drive shaft related. (U Joint, front drive shaft bearing, rear coupling or the drive shaft itself. I do not think Pinion Angle and phasing of the U joints has anything to do with it if you still have the original Torque tube.
As recomended before, I would lube the U Joint and if that does not take care of it, the rear end may have to come out of the car. If so, check the front drive shaft bearing and outer race and also the end of the drive shaft where the bearing rides. Often this stuff is worn out. Also check the U Joint for wear and the rear coupling where it fits onto the end of the pinion. Also check to be sure the drive shaft is straight. If everything looks good, you may want to take the drive shaft to a drive shaft shop and have them check the balance.
Let us know how you make out,
Chris