After doing some research I finally decided to look for a Borg-Warner T-18A manual transmission.  Manual because that is what I prefer.   The T-18A because of it's 6.32:1 first gear and it's heavy duty, cast iron construction.  Also T-18 is probably the most common transmission to swap into a Jeep because it is heavy duty, relatively inexpensive, and it can be swapped in easier than almost any other transmission and several companies make adapters for use with the T-18 and T-18A. The earlier T-18 has the same heavy duty strength but with a higher 1st, 2nd, 3rd and reverse gears but the later T-18A had a better set of gears so that's what I was looking for.  The T-18A version was used from 1977-1979 in CJs but are rare finds and if I had found one I'm sure it would have broke the budget if the seller knew what they had.  T-18A are common in other 4x4's including J-20 pickups and Ford trucks and both can be converted to CJ-7 use.  Both T-18 and T-18A versions have a PTO port on the drivers side. Identification of a T-18A can be found with the casting number on the drivers side of the T-18 which is T-18 or 13-01. The T-18 has a 1 1/8" 10 spline input shaft and a 1 3/8" 6 spline output.   

Through a contact of Bob's I bought a T-18A mated to a Dana 20 Transfer case that came out of a J-20 pickup and was in good shape.  Because of the length of the J-20 pickup Jeep used a 5 inch adapter between the bell housing and the transmission giving it a long input shaft.  Mike from Jeepfan.com had done the same swap and he gave me the info I needed to find a short input shaft kit through Hick's 4X4 in California which is currently on order.  Also on order is a T-18 rebuild kit to replace the gaskets and bearings.

One of the first things I did was clean off the build up of road grime.   I borrowed a friends high pressure power washer and through a combination of carb cleaner and Castrol Super Clean I blasted off the thick stuff.  As soon as it dried later that day I then primered the whole thing and painted it gloss black the next day to prevent it from rusting without the protective layers of oily dirt.  I did this before the rebuild because I  figured it would be easier to work on it without all the dirt on it and the painted surfaces would clean up easier than trying to remove the gear oil after a rebuild.  Also blasting the transmission and transfer case probably forced water into the old seals and the breather and I'd rather do that before a rebuild rather than after.

Soon after I removed the adapter and bell housing, exposing the long input shaft which will soon be replaced with a shorter input shaft.  Also the transfer case didn't shift correctly due to either the stick shift of the transfer case or something inside the shifters base.  Mike had a couple of extra Dana 20's lying around so he graciously donated one with an identical shifter for parts.  Thanks Mike.   Notice the dust that covers the T-18A and Dana 20. That's because of the tub work going on in the garage.
The Donor Dana 20.
T-18A rebuild and a Short Shaft replacement

    

Project CJ-7 ~ The Transmission

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