I'm putting a 98 4.0 block into a 91 MJ.....as for the computer issues, I agree. Some of the sensors in the intake manifold will swap...IAT/TPS sensor for example. Although these engines have different power steering mounting patterns on the intakes. You will need to use the 98 intake manifold to retain all the sensors, fuel injectors, fuel rail and throttle body, as they are different from a 91. Just swap all sensors from the 98 engine to the 91....it should be pretty staight forward.
Also the fuel pressure for a 91 H.O. is 39 PSI I believe and for a 98 it will be 49 PSI. 91 fuel injectors are supposedly rated at 21lbs/hr. A 1998 is rated at 23.3lb/s an hour...they have grey terminals on the injector.
Hope this helps!