if its still there in neutral that eliminates the engine and pretty much the whole trans except the output shaft, which is unlikely. i would try disconnecting the driveshaft and reinstall it 180* from where it was, and see if it changes anything. also, you can find a good auto shop or ford dealership w/ a road force tire balancer, and balance them on that machine, it can tell you if there is a bad tire or not, its a really great machine.

 

Is it a new tranny? because i had the bushing go bad in the tail of the tranny and it shook on the freeway.

 

Drive line bolts coms loose alot and make the driveshaft vibrate, easy check.