Check ALL the rubber hoses including the 4 short ones on the passenger side of the throttle body to make sure you don't have a vac leak.
The idle (fuel/air delivery) is controlled by a couple different sensors but mains ones are MAT TPS CTS WOT MAP and idle air motor. All these have potential to affect the idle so break out your multimeter and start testing them. If you don't know the testing process let me know and I can post them.
Mechanically, it could be too much fuel pressure which should be around 14.5 psi. Test port is an Allen plug on the driver side of the TB by the vacuum booster check that with a standard pressure gauge and a Schrader valve
89 YJ S, 2.5L/AX-5/NP231
99 WJ Limited, 4.0L/42RE/NP247
93 YJ, 4.0L HO/32RH/NP231 - Sold