Others have swapped in an HO in place of a RENIX motor. I am doing it also, but I am replacing the electronics to a '95 specs. I don't think you will have to do that. Here's a link that might help:
http://www.rockmodified.com/2003/april/TB/tb_perf.htm
A few words of caution, First is if you need to retain the EGR setup for smog checks. The HO's don't have EGR. SO if you need smog emmisions, then you'd need to retain the EGR system or change the complete wiring to 91- and up. I think there was a discussion on this many months back and most though to cut out and weld the EGR boss section into an HO or 99+ manifold.
You might want to update the cooling system to an open system at the same time. Check Cherokee America's website. You might need a newer exhaust manifold or redrill the holes to your present one. If you have after market headers, then this should be a problem.
You might need to think about the throw out bearing or pilot bearing on the tranny. They changed through the years. For certian swaps, and I think yours is the the particular years, Advanced Adapters sells the only bearing for it. Check this website, it might have the bearing info:
http://www.jeep4.0performance.4mg.com/stroker.html
Also, 99+ heads are a more restrictive than earlier heads on the exhaust ports. 96+ blocks are suppose to be a bit more sturdier. Up to 2000, your motor mounts should/will swap directly. I have a 2003 block. I had to modify one of the motor mount brackets and use a spacer with the other. The '03 block also had the newer (better) style of water pump. They have a different bolt pattern than earlier water pumps.
My setup is an '03 block with a '95 head and an NV 3550 tranny and '95 wiring. '95 is the last year for OBD I. And a '99 intake manifold with Clifford ceramic coated headers. I also had the intake manifold ceramic coated. Its not running yet, but hopefully soon.
If you were closer, I have an '88 4.0L sitting in my garage. $100. It ran OK, with some ticking, from the lifters I think.
Tom
Knew I forgot something. The fuel rail is different between the years. The Renix one won't bolt up to later year manifolds. Also the fuel and fuel return hose connections are in different locations. THe Renix has one front and rear. The HO's are both at the front. I think the fuel pressure regulator is different spec too. 96+ are different also. I think only one fuel port. If you change electronics, then you'll need to probably change fuel pumps. I bought a '95 fuel lines for mine, the metal lines. I need to adapt the rubber lines though.