This is totally random, and it is just a suggestion. I had the same problem last few weeks. 1997 jeep grand cherokee, 102,000 miles. I checked throttle body, idle air control (go through all that, very easy to clean and check) transmission, etc. It wasn't anything I could visualize and or troubleshoot. Took it to the shop today and they were airing on the side of electrical. All it took was the mechanic to knock the computer module and it stuttered, it was a connection issue or a broken pin. During start/stop and while driving off highway where the road has more bumps and such it would shake and cut out on me. We were going to replace it, but after taking it off to inspect (he couldn't check and re-soder, chrysler put a goo jell in there so you can't do anything with it) and replugging it back in, the jeep works fine. I'm just going to see how it performs over the next week as the computer modules are a few weeks out at the dealership and at least in the 1997 is a dealer only item.
Something to check out, its supposibly common in the mid 90s jeeps, and can present with a whole bunch of symptoms, I dont know about the KJ but it might be an idea.
3.5 inch lift
(all the steering goodies/upgrades)
Crager soft 8-32x10.5x15 AT
Kevinsoffroad Radiator support/tow hooks