Vibration problems like that can drive you crazy. I'm not aware that the driveshaft length is different between manual and automatic transmission. Since it doesn't change when you depress the clutch it's probably a safe bet the problem is alignment or support.

Two thoughts: 1) double check that you got the u joint caps seated properly on the 3rd member yoke. 2) You didn't mention the condition of the 4 speed. I'd be concerned about the brass bushing inside the tail stock of the 4 speed which the slip yoke goes into. I've had high speed vibration issues because of those being worn, but often the vibration will over power the rear seal and you'll have fluid leaking out the back of the tranny.

Hope this helps.