Thanks for the suggestions. I massaged the lip down nice and evenly with a hammer. Got the tranny all bolted up then snugged up the mounts (Had to undo the motor mounts and jacked the front of the engine to line the tranny). Now I've got about 3/8 to 1/2 inch clearance.
Now I need to shorten my shaft about 3" and I'll be good to go!