I have a 98 jeep cherokee 4.0 I6 with AX15 tranny and NP231 TC. Roughly 125k miles. The only engine mods have been a cat back exhaust. Whats happening is when the jeep has been running for a while, like at least 30-45 min, it seems to loose a bit of power. It seems like I have to slip the clutch a bit more from a stop to get going. The loss in power is very small, but I notice it. The engine temp never goes over 210, and it doesn't seem to be related to engine temp because it runs fine at normal engine temps for a while before I notice the power loss. I brought it out to college in Colorado, from California. So it went from about 1k elevation to 5500 ft elevation. It ran horrible the higher in elevation I got on the way out, but I disconnected the battery to reset the ECU, and it ran like normal when I started it back up.

Anyone have an idea of whats going on here? Can I get the ECU tuned for higher elevation? Am I loosing compression?

Your catalytic converter may be starting to plug. Have an exhaust shop check it for you.