Playing devil's advocate...
It wouldn't make much sense to go that far and only change 3rd gear. A complete rebuild kit sells for ~$350 at Morris Jeep - but that is Crown (C.R.A.P.) I don't see seals or gaskets listed on the included parts list - add another ~$200. That's $550. Different (better quality) brand would add to that price. So let's say materials, all in, is going to run $700. Now you have to pay for the labor to tear down and rebuild. With a $50 labor rate and 10 hours (guess), you can add $500 more. You're already $1000 to $1200.
Have you looked on Craigslist for used Jeep 4.0 with a manual. For the price of a rebuild, you could get a parts Jeep.
Just my 2¢.