89 Spirit ES, 2.5 Turbo, 523.

I just did a 2500 mile cross country run in my Spirit, and the car ran fine. But towards the end of the trip, I began to notice a thumping vibration in the front end, only when under acceleration, like a tire was WAY out of balance or out of round. But it feels more like it is in the drivetrain because the whole front of the car shakes a bit.

And now that I have gotten here and the car is mostly unloaded, I drive around and notice it even more now. Under cruise and coast there is no vibration, but when accelerating it starts.

Any idea what it might be? A CV joint binding up? The outer right joint has its boot torn up a lot and there probably isn't much grease in there. I recently dropped the transmission out to change the clutch, I wonder if I somehow reinstalled it not in the same position (passenger motor mount was never touched), and now the axles are not properly centered and one is bottoming out a bit?

Any ideas?