VIBRATION SOLVED!
After going through and inspecting everything over again, with numerous test drives and configurations, Dial indicator run-outs on the yokes indicated nothing bent. So, I narrowed it down to the drive shaft AGAIN! I took the original shaft into Inland Truck Parts in Olathe, Kansas and had it balanced after my first set of new u-joints. That didn't solve it. I then switched to Spicer sealed u-joints, that didn't fix it. I went back to Inland for the balance again. Ended up buying a WHOLE NEW custom shaft with new spline yoke and a shiny new harmonic disk. THAT made it worse! I didn't see any weights this time, so I was suspicious. Then I read there was a Jeeper guy named Ron Istas at the Missouri Inland Truck facility. I called Ron and made an appointment, telling him I was suspicious of what the Kansas store had done. Ron drove it, felt the harmonic and had me pull the shaft. He and his team put it on the balance machine (Fantastic facility) and spun it up to high RPM. It was well within tolerance, they even tacked on a small weight to make it perfect. I reinstalled it and Ron drove it again. No improvement. So after a lot of thought, Ron said, "it's got to be that big harmonic balance disc causing a frequency to set-up at 50mph. Pull it off this weekend and see if it helps".
Yesterday, I pulled the shaft and precisely knocked off the disc with a BFH, reinstalled the shaft and went for a drive. IT'S GONE! No vibes at 45-55 even under acceleration! All this work and money and that's all I really needed to do. REMOVE SOMETHING, not add a new everything! Again, Ironic that something intended to reduce vibrations was actually causing them.