You do have a lot of issues., As for the clunking noise, if the ujoints are fine (ie: no play when turning the driveshaft both ways quickly) and not your trans mounts, it is from play from somewhere. I would next check, as Chris said, pinion yoke. See if there is any play in the yoke gear and pinion gear. By playing around and thinking about it, you should be able to diagnose it.
SgtDel
aka "Andy"
www.delbridge.net
1979 Big 10 383 stroker
1991 Blu 'Burb 3/4 ton 4x4