Your description of what spins with what is only accurate with the engine running and the clutch disengaged (that is, the clutch pedal pushed in). When the clutch is engaged (pedal out) clutch disc, pressure plate, flywheel, tranny and engine all spin together.
I'm guessing a pinion bearing problem. Sometimes gear installers get the preload or other settings wrong. This can wear out the pinion bearing and/or cause excessive vibration.
I once bought a used Bronco that had a loose pinion flange. Once I figured that part out I tightnened it to specs and the vibration was cured.
Could be a similar situation or just a plain bad gear install.
Your description of what spins with what is only accurate with the engine running and the clutch disengaged (that is, the clutch pedal pushed in). When the clutch is engaged (pedal out) clutch disc, pressure plate, flywheel, tranny and engine all spin together.
I should have been more clear. That is what I meant. And, yes, I realize it all spins together with the clutch engaged.
Anyway, I have better news. I turned the driveshaft 180 degrees and bolted it back up and the vibration was cut by half. I am going to rotate it another bolt hole and see if it gets better still and repeat until I find the sweet spot.
I have checked the differential fluid and its free of metal shavings and the backlash on the gears seem fine- Everything rotates with no sticky spots or noise, so I am hoping to rule the gearset out.
Yes. I have already mocked it up and thought that I would do 180 first. There is 8 bolts holes in the tailshaft and the yoke will bolt up in all 8 positions.