Before embarking on serious changes to your cars wiring. Would you mind providing more info as to why you feel you need a new harness?? i.e. lots of splices, wrong harness for the engine
Also, Would you mind elaborating on the source of this "new" engine. Is it from a different car? Is it a JDM Engine? Is it the original engine that has been rebuilt?
As for the original question, More than likely not. The reason being, the multitude of harnesses used in 89 cars. As far as ECU to Engine. There are no problems. There are several plugs on the ENGINE side of the harness that don't plug into the ECU. These plugs attach to the CAR HARNESS.
Most notable of these is the B1 Plug. It is the largest of plugs that DON'T plug into the ECU. This connector goes from the ENGINE HARNESS to the CAR HARNESS. It has numerous important connections such as the ignition switch, starter solenoid wire, gauges, and other such dash related stuff.
A Comparison of pre and post 89 connectors.
http://members.shaw.ca/boltz/7MGTE-S...TE,%205MGE.htm
Now, here is where it gets tricky. An 88 harness B1 Plug may plug right into an early 89 CAR harness, however, I don't think the wire functions match up 100%. I put an early 89 harness into my 87 car and had to change 2 wires and everything else was golden. A later 89 harness would require much more significant modification to make work to the point of chopping the whole B1 plug and re-doing the whole plug.
Step 1: With the battery disconnected. Place your 88 harness in the passenger floorboard. Try to plug your 88 Engine Harness B1 plug in to your 89 Car's Dash harness. If it slides right in and clicks. You may be able to de-pin a couple of wires and move them in the plug to make things work correctly. If the plugs are not compatible. I suggest you find an alternate 89 harness as the differences will be significant.