Stock trans mount/height??solid/poly mount??
Maybe the rear axle housing bent.any problems sliding the axles in/out??
Posible bent spring/making thrust angle off.rear wheels pointing more 1 way then the other.(dog tracking)
Do you buzz the engine to the same rpm in 1st and 2nd??
Switching to 3.23 gears made the vibration come at a higher mph,Then It has to be rpm related
A shot in the dark.the fan???
A cracked flywheel will usually make some noises
tailshaft bushings ok??
Vibrations can travel.What if the vibration is up front of the shaft,but the rear u-joints go bad because there is no room to move/ more tightly held together.
Have you had it on jackstand,and whatched the driveshaft,should be pretty smooth,any osilation.
just thinking outloud.