rjones
Here I go again, jeeze!
The thing that bothers me, is, in your original post all was fine prior to the u-joint change. Maybe they are all bad. If a u-joint is tight on install, tapping on the yoke near the joint cap will "seat" the cap tight to the snap ring and will free it up.
How many miles on your truck? Is it a standard or auto?
If the motor mounts get bad they can cause alignment issues as can the transmission mount. This can throw the angle of the short shaft off, maybe this caused the mis-alignment? The crankshaft angle, short shaft angle and pinion angle need to be the same. The long shaft angle don't count.
If your center bearing is good, you can just change the rubber. Most parts houses carry them or can get them.
Nick