I used to have a bad vibration that started around 70mph. Turned out it was a bent driveshaft. So, after finding another one at a junkyard, I installed that one and no more vibration. Then my T5 breaks and I put another tranny in, and I notice the vibration at 70mph again, but not as bad this time. I rotated the driveshaft 180 degrees and the vibration was gone again. However, now the vibration comes and goes.

For example, on a 2hr trip, for the first hour it had the vibration, then magically the rest of the trip it was smooth and nice. I'm planning to replace the driveshaft again, but does anyone know what could be going on?

 

u-joint or tail bushing?
If they check out you can check the balance on the drive shaft by putting a large hose clamp on the shaft at the rear and test driving it. If it is smother the shaft is out of balance.
If it doesn't get better on the first try, turn the clamp 1/4 turn at a time on the shaft and keep retrying. You can also try it on the center and the front if there is no change at the rear.