For what it's worth my Challenger has the same type of vibration. Bell housing is with-in .005" in both planes. U-Joint angle is 1.5 degrees at both ends of the drive shaft (one angle positive,one angle negative),new Dyno-tech shaft with less than .030" runout, 2 different sets of axle shafts. I've had 3 center sections in it,2.76,3.55,4.30. No vibration with the 2.76. Both the 3.55 and the 4.30 have been in my other car with no problems. I rebuilt the trans, no noise, shifts great. However back in the day I broke 3 drive shafts. One broke a bell housing, one broke the front driveshaft yoke. I'm wondering now if the input or output shaft/shafts are bent. I wouldn't have thought it posible,but. This summer my friends 66 Coronet lost a u-joint cap on the X-way at 55 MPH with 4.10 gears. It bent the output shaft at about a 20 degree angle. Though it was an automatic the shafts are similar in diameter.
I haven't got around to checking it yet.
Doug