Headers not fitting after engine removal

The motor mounts have slots and are arranged in a wedge so the engine can "rotate" slightly as well as tilt with a spacer. Don't forget the possibility that when the exhaust was installed, it wasn't "pushed" into place down at the pipes. Sounds like from your description the engine is either tilted fore/aft, or left/right, or both. Someone suggested the motor mounts being in the right place. It's possible to moint them on the wrong side (left/right) as well as the wrong side of the bosses on the engine. Just things to check/ponder. if it came out, it will go in. But something changed. Trick is figuring out "what"....