Rubicon engines

Just wondering how similar the 2005 rubicon motor is compared to the 2001-2004 models. I know they changed the body style I just forget if anything else was changed. I need a manual and the clymer manual says 01-04. And on a side note. My dad was pulling a heavy steel beam to drag his driveway and had it in 4wd low range and it made a clunk or cracking sound and he said it would not move. So naturally he pins it and it broke loose but clunks when he drives. So he took the body work off and parked it. He says the tranny is shot. But it still drives. Anyone have a better idea what it could be