I would doubt the shaft would bolt in backwards, though never had the urge to try it. The u-joint goes on the rear half, so you have it right.
If you have new flex disks, a good center bearing/ support, and have the bumps aligned on the two shaft halves; then it might be the u-joint.
How does the joint feel? Does it have the slight "detent" when moving off center? Mine used to have the detent at about 100k,, but I checked it last fall, with 200k, and the "detent" was gone, just very smooth through it's movement (probably getting sloppy, just not enough to feel by hand).

Do you have the front flex disc on right - German wording facing the driveshaft.

Are the front and reat alignment bushings on the shaft ends in good shape? They usually last a very long time.

I've been fighting a vibe that occurs under accel at 18 MPH, only when hot.
I went thru all the driveshaft stuff except the u-joint, and never had any effect on the vibe - but yours sounds like a different animal.

Let us know any progress.

DG