I also did a YouTube search on Cherokee 4.0 Exhausts and found several Flowmaster Super 40 videos. They do sound pretty good. I'm thinking that route as well. I plan on calling my shop tomorrow and asking them for the number to the exhaust guy cause they don't do mufflers and stuff in house. They had a guy weld the cracks in my exhaust manifold so I, like you, plan on calling him up and talking to him. See if he has any recommendations. I'd like to find a muffler cheaper on CL or eBay as I'm guessing if I buy it through the shop it will be quite a bit more. I found a Flowmaster Super 40 NIB and the price is good, but the in to and out of pipes are 3" which I think is way to big.
There was also some nice sounding Magnaflow exhausts too.