You can try Z&M Jeeps. They sell body panels. I picked up a driver's side rocker panel at a Jeep show in York PA.
http://stores.zmjeeps.com/rockers-quarters-bed/
I do not recommend the bedside panels. They are not stamped for the flares
The tcase is universal. It doesn't care if it mates to a manual or auto.
One issue to consider is the spline count for the trans that the tcase was mated to. For manual trans, the BA10 had a 21 spline output shaft. The AX15 had a 23 split output shaft. So, the tcase input shaft needs to match the trans output shafts. For manuals trans (4.0 engines) the change from BA to AX occured in mid-89 when Jeep changed trans. You will need to get the tcase for the year of the trans.
For AW4 -
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¢.
The AX15 will bolt to any Jeep 4.0.
One issue you may have the pilot bearing/bushing for the trans input shaft. Early years trans have a smaller tip than later years tip.
Someone else may comment, but I do not believe the bellhousing that bolts to the 4.0 will bolt to a 2.5. The bolt patterns are different.
You may have to search for a Dakota bellhousing. Do some searching for the years that match.
I would jack up both sides at the same time. Remove the wheels and drums on both. While working on one side you have the second to reference. Better than a picture on your phone. You have a 3D model to refer back to.
Also, brake shoes are directional - one leading, one trailing. I can not remember which is which.
As you take the pieces off, lay them on the ground in front of you in the same orientation. This will also help you put it all back together.
My brother used to work a parts counter at a Toyota stealership. He always talked about a time he sold a small part ($10 retail) for 3x that price. He told the customer it lists for $50, but he will sell it for $30. The customer was grateful.
I am always skeptical when I go to the dealership. I remember my brother's story.