At this point, I would take a good look at the transmission, and motor mounts for the rubber showing signs of breaking down.
When you check the u joints, did you remove the driveshaft and check the smoothness of the bearing caps, or were you just looking for missing/rusty needle bearings? I've seen a lot of the needle bearings cause step marks on the cross shaft that didn't have missing bearings or show rust, yet. If you drop out the driveshaft and any of the u joints don't turn smoothly and freely, replace that joint.
Have you checked the condition of your front wheel bearings?
Have you checked to be sure the pinion nut on the rear end has not backed off a bit? Gene