I have had a lot of interactions with the folks at Vegas 4X4 and Dan’s Driveline over the years with my Jeeps and both are excellent in what they do.
That being said, with Jeep using that 4.0 HO I6 from 1987-2006, any mechanic worth their salt should know how to work on it, so anyplace you go should be able to do it. If you were so inclined to do it yourself you would most likely have really good success between the helpful info on YouTube and JeepForum.com.
Milford Automotive on North Decatur is a good place with an owner that is honest and fair - you might want to check with them to see if they can provide some insight as well.