John RR has the right answer.
Here is a picture of the rear middle threaded hole on the case. You see that it has a counterbore where the top few threads would normally be. The longer shoulder goes through the cover and into this hole to line up the cover.
Go here for a service manual:
http://www.mymopar.com/index.php?pid=109I would recommend that you don't try to rebuild the trans without an appropriate service manual. The procedures are slightly different for standard, Hemi box, and OD4 Transmissions.
Robert