If you have the engine, computer, and engine wiring harness (including all under hood components like the power distribution panel), you have almost everything needed to make your life simple. I always recommend that people take the cabin-side firewall connector half along with a few inches of wiring so that you have something to splice to, now you'll need a detailed pinout of the Jeep and new motor harness firewall connectors to determine what you need to splice to what. I cut off the Jeep connector after marking each wire and then mark each wire on the new-engine connector. Now splice these wires, function to function - you shouldn't have any "important" wires left over on either side and these can be addressed one at a time. The critical set of wires will be those that allow you to turn the power on with the key switch, this will power the computer etc.
Depending on how the new-engine wiring harness was put together, you might need some creative splicing for things like headlights, fuel pump, etc, but if you have the connector pinout descriptions for the new-engine harness and the old jeep harness, you should be able to see exactly which wires to cut and where to splice them - it's no different than plumbing.
I would offer you some diagrams but the oldest I have for the jeep is '91 and the newest I have for a GM truck is '96. If you can get some diagrams that represent the correct jeep and new-engine connectors, I can help you with what you need to do.