You will need to probably keep the wiring clips that match up to the ECU and the other plugs under the dash. You can remove the wires by moving the lock pin in each one, and pulling the wire out without cutting it. You will than need to figure out which wires from the JZ harness will go where in each clip. 92TealSupra may be able to help you with this. Send him a PM. He helped me turn my 89 harness into a 92 for my new body, and he enjoys helping with wiring swaps.
***EDIT****You probably won't need to worry with the ECU plugs, as the JZ wiring should match the JZ ECU. But the other plugs nearby will need to be addressed.