Maybe you have a problem with the frame sagging or the front or rear motor mounts. Last year I installed my 28 U joint cover with the tab on the top half and it cleared the middle crossmember by about 3/16", give of take 1/16". I would suspect that maybe the front motor mount maybe too high, causing the U joint cover to be too low. Does the front crank hole cover correctly line up with the crankshaft ratchet nut?
Rusty Nelson