Why do you say your tranny is bad? A lot of 42RE problems can be solved with replacing the pressure sensor and solenoid....
Anyway, the OBD-I vehicles had a TCM to control the 42RE.... A 99 WJ I think used the 45RFE.... You need a ZJ tranny.
RockAuto says for the 1999 Grand Cherokee Laredo 4.0L is a 45RFE....
Any ZJ with a 4.0 should have a 42RE... Some had the AW4, but they are VERY obvious differences between the two.. (look at the tranny pan).
If you feel brave and adventurous, try rebuilding the trans you have. They are fairly easy if you can read, use tools, and have a good set of snap ring pliers... The only thing you need a specialty tool for is the OD section. The direct pack is under 900lbs of spring pressure, and requires a special tool and a press to compress the pack to remove the snap ring. Upon reassembly, you need an alignment tool to keep the internals lined up.
Me and a friend of mine rebuilt my 42RE in an afternoon. (Three days total... pull one day, rebuild one day, install one day). New torque converter, new clutches, new steels, new seals, and new solenoids.... About $350 total parts... and I had to replace a couple of thrust bearings and I optioned to replace the direct spring.
Mid-Florida Jeep Club - Member
1996 Jeep Grand Cherokee, 4.0L/42RE/242 - Rebuilt motor w/ Comp cam (4/12), 3.5" Junkyard F>R lift, 31x10.5.x15 M/T's, Spartan Locked D44a, TC & tank skids, F&R adj trackbars, V8 steering arms
Galaxy DX99V CB, 102" SS Whip, Yaesu FT-2900R 2m, Larsen 1/4w mag mount, Sony HU, Massive 3way - F Door, Pioneer 3way - R Doors, MB Quart ONX304 Subs (x2), Lanzar 1600w amp.
"No Matter Where You Go... There You Are."
"Oh me oh my a lovely day is dawning. Oh what a joy I didn't wake up dead. So I can go to work and then resume my yawning, and get my sleep on site instead of in my bed" - Daria Morgendorffer (with my twist)
You can use a tranny from a 93 to a 98. I'm currently running one from a 96 in my 94. Note; some 93 ZJ's have a different auto. Easiest way is to compare the transmission pans. The 93's I refer to look incredibly different, so it could easily be spotted in the JYard. Sounds as though you may already have one lined up, but there is a reason you cant use a 99+. I cant remember right off hand, but Ill look and see if I can figure out what it was.
Edit: Seems its the sensors and connectors that are different. Other than that, they are pretty much the same. If you cant change them, I wouldn't know. Maybe someone else can chime in.