So recently after replacing my clutch after i engine brake in 2nd or 1st gear coming up to a stop when i push in the clutch the jeep will stall unless i blip the throttle while trans is disengaged. I've also noticed the exhaust smells incredibly rich, like make your eyes water standing by it rich. Is this a vacuum issue or did something happen with my O2 sensor when i took the upper exhaust off and on?

EDIT: Solution was new throttle position sensor idles just like it used to after deceleration no stalling anymore

 

It's possible. Hook a voltmeter to your O2 and see what it's reading. Or just replace it if it's got some age on it.

This is also a problem that occurs when you use an automatic ECU on a 5 speed (at least in the 98)

 

Look real closely here:

 

Update it's now so bad it will not stay running after disengaging the clutch even if i don't let it engine brake. I'm suspecting MAP sensor because it got worse last night after I mashed the throttle and it started to cut out real bad. but O2 and MAP I'm going to replace both because i think they're genuine 1994 mopar still.

 

I just remembered when i swapped my t-case i didn't get the speedo gear reengaged with the shaft. Would that cause an issue maintaining an idle?

 

Ok I've completely figured out my issues. I had an unplugged throttle position sensor and an exhaust leak so bad none of the exhaust was actually passing by the oxy sensor. after plugging the tps in and getting a new exhaust donut the XJ runs well again still stalls if you let it but as long as i blip the throttle it won't die. Next step for me is to stop all vacuum leaks and it should be back to normal