I ran a Magtec-Hytech pan on my diesel truck for extra cooling. Worked fine, greatly increased the fluid capacity.
I wouldn't bother on a Jeep unless you plan to tow heavy and often with it. It would reduce ground clearance, something to consider if wheeling it.
5.9s didn't come with an external tranny cooler so I would add one if I were you.
My mom has a bone stock 5.9 that has 320,00kms on it, she bought it with just under 200,000kms. In the time she has had it she's never done anything to the tranny, not even changed the oil and its still drives like when she got it.
My 5.9 I bought with a bad motor almost 4 years ago. I replaced the motor and added an aftermarket cam, intake manifold and CAI. The tranny is still stock and hasn't ever made even a hiccup. My suggestion is to get yours rebuilt buy a reputable shop and ask them about a shift kit or something equivalent and add a good cooler.
Unless you plan to add BIG HP you don't need to go nuts on the tranny. Save that money for something else.