Reading through this string I have a couple of ideas that might help;
1. When a new problem develops after I work on something, I go right back there first. In this case, you may find one of the new u-joints is bad. Seems like these days you have to suspect even new stuff.
2. Did the u-joints seat all the way into the yokes? If there's a grease fitting, is it pointed the right way or is it hitting at some point in the rotation?
3. It's possible that at the slip yoke there's a build up of old dry grease and dirt that won't let it slide all the way in.
4. Sometimes new grease can seal the splines on the slip yoke and so can add pressure so the driveshaft doesn't slide forward as easily and can act like the dry grease thing too, but it goes away until you extend the driveshaft again, which happens every time you flex the suspension.
5. Wheel bearings going bad are like a fast vibration and can sound almost like a train or like running mud/snow tires on asphalt. Especially with the rear you may not feel or hear anything with the tires off the ground.
6. There is mention in the string about the exhaust being a possible culprit. I'd suggest wedging the pipes where they go through the frame with something that won't catch fire or melt and see if the noise changes. This isn't to "fix" it, just to see if it changes.
7. If while you're under it looking, the wheels are off the ground and the full weight isn't on them, you could miss seeing the problem, especially if the axel is hanging down.
8. Did anything fight you while taking it apart? Maybe if you had to beat on something, it got tweaked a little?
Hope this helps and you find the issue quickly and it's easy to fix. It is possible that a new issue just happened to start right after the u-joint and motor mounts were replaced, but the odds are against it. I'm supposing that there was a problem causing you to do the work in the first place. If so, did the work change the problem or create it?

Life isn't about arriving at the end in a pristine, well preserved body; It's about sliding in sideways, all clapped out, yelling "What a ride!"