Usually they balance the shaft with the yoke, but there's a possibility the inside dimensions could be off a slight bit which would make it ride differently in the tranny. Did anybody take a dial indicator on the shaft just after the front yoke while it was mounted to the tranny and see what the runout is when installed? That's one of the first things I check, some guys use a piece of chalk held against the spinning shaft, but the dial indicator is more accurate. Turn the shaft slowly without touching it. Put the tranny in neutral and rotate the tire so as to turn the shaft slowly. Also, move the shaft up and down and side to side to check both the joints and the play in the rear bushing of the tranny. You checked the angle of the pinion to make sure it matches the angle of the tranny in a vertical plane, did you check the alignment in a horizontal direction? Not usually off, but it would be a shame to assume it's correct and find out the rear is slightly angled or the tranny is angled because of a miss-stamped mount. Rare but possible. I'd be checking the runout and play of the front while installed.
You were typing while I was also. Do you have a picture of this installed in the car so we can get a better idea of what may be going on?