The only real issue is the injnition coil rail. Some have made brackets to adapt them on. Possibly the cam from a timing issue. I am not real sure on that though. I would use the 2000 intake. A bit better power. You will need to use your '93 exhaust. All other bosses and mounting points should be the same. You only get into problems on the '02 amd up GC blocks. I have one in an '88 Comanche. The motor mount bosses are a bit different. But adaptable.
I have had an '88, '95, '00, '03 and do have a '98 motor. I didn't see any differences as far as mounting of the motor mounts and other stuff on the '88, '95, '00. I haven't taken out the '98, but I doubt there would be any differences. I'd also reuse the accesory drive belt brackets from the 2000.
Tom