I can't remember the exact details, but I had a friend put their mounts onto the frame incorrectly, resulting in the motor sitting about an inch forward. I honestly can't remember how they did it, but I will tell you I was there to lift the engine, and put the mounts back into the correct locations/holes. The frame was out of a Firebird, not sure if that was part of the problem or not, just remember the whole thing was a real PITA. Can't speak to the cross shaft, car was an automatic.
I'll actually see that car in June, I'll take a look and see if I can see how they had made the mistake in the first place.