I may have found out why this search is gonna take a while. There is a 5 speed up for sale right now on ebay, sitting at $200. Has a reserve. This is what got my attention, the listing says:

"This is one of the rarest models produced since less than 3% of XJs came with an Aisin-Warner AX15 5 Speed Manual Transmission"

No freaking wonder I can't find one. I don't want the 2 door but it has low miles, 94k. Gonna wait a few days see if it gets bid up, if not I'm going to try for it. Maybe it won't skyrocket above $200 too much, it's a '97 and a dreaded 2 door. Here's the listing. I do like the color.

http://www.ebay.com/itm/Jeep-Cherokee-Sport-Utility-2-Door-1997-jeep-cherokee-xj-sport-utility-4-x-4-5-speed-2-door-very-/111594878381?forcerrptr=true&hash=item19fb92b5ad&item=111594878381&pt=US_Cars_Trucks

 

300k miles is nothing on these motors. you should broaden your search a little bit. miles shouldn't be a worry.

 

6 days left I see the price jumping to 4-6k especially with 93k on it.
The ax15 was used from late 89 to 99 then the NV3550 was swaped in for 00 and 01. So not rare was standard transmission. Second it's was repainted at one point and time reason why?
The 2dr and being a 4x4 it a somewhat of a rare part at least here it is.
If you want something that your going to take off roading only, I'd look into a older model anything above 91 thru 95. The you still get the hi output motor same trans, can find a 4 door a lot easier. I have one sitting in my yard that's being used for a storage for other jeep parts. Junk yards are usually stocked more frequently then newer ones, body's from 84 thru 95 didn't change, all look the same till you open the hood or look at the seats.
Now downside most had a 35 rear axle as this one does as well, not a favorite axle, some had the 27 spline 8.25 vs the 29 8.25 that the 97+.

If it was me I'd keep looking and spend what you can possible fix, but then again I work on everything I own and only take it in for tires, emissions, glass work, and alignments depends on which vehicle.

Found 2 so far one with 121k another with a rebuild with 40k.
1998 Jeep Cherokee Sport 4.0l 5 Speed Manual - Used Jeep Cherokee for sale in Keedysville, Maryland | Trucks2Cars.com
http://www.trucks2cars.com/car-detai...580231151.html

1997 Jeep Cherokee 4x4 4-door 5-speed lifted
http://tuscaloosa.craigslist.org/cto/4848826309.html

 

That $200 is now bid up to $4550. And still 5 days to go yet on the auction. Thanks for the links, I'm taking a look at them.