YJ's had 3 manual trannys:
4 cyl models had the aisin-warner AX-5
Pre 1990 6 cyl models came with a Puegeot BA 10/5
Post 1990 6 cyl had the aisin-warner AX-15
As you could guess they all stunk, but the BA 10/5 was one of the worst

trannys ever made, the case was even 2 pieces split down the center lengthwise!
The AX-15 had bearing issues which would case the whole gear assembly to wobble and not shift. Also had a leaky output shaft that if not fixed would of course burn the whole thing up. On top of that the throw out bearings would wear out constantly and require pulling the whole transmission. That being said it's the best out of the 3.
If he's got the BA 10/5 hear is a decent write up on a swap to the AX15
YJ Trans swap, BA-10/5 to AX-15 ** Write Up - JeepForum.com
Anyway he looks at it he's pulling the unit and will loose much skin off his knuckles. Make sure he's got a set of Torx as the bellhousing has 3-5 different size bolts with some being torx IIRC. Also will need long extensions and multiple flex joints to get at the top bolts through the shifter hole.
While he has it out I would highly suggest he does the conversion of the NP231 and loose the slip yoke and check the slack in the chain. Also go ahead and change the clutch, throw out and slave cylinder while you're at it.
Hope this helps, once I get a tranny out I usually let a pro deal with the insides.
PS Also introduce him to where the ignition module is and have him carry a spare.