Driveshaft phasing? If you pulled the shaft to swap all 3 u-joints, did it go back together in the same splines? I had a driveshaft built for a project once were the u-joint was off by about 1 degree. That caused a pulsating vibration as described, however at about 55mph. It was also bad enough that the shifter would vibrate to the same frequency that I was feeling with my backside. After going down the same paths, I took the only thing left to check to another driveshaft shop. They repaired the shaft, balanced it to a higher spec and my cyclical vibration went away.
Just a thought
Scott