Just did this job. Even with a new harness, there is a lot of rewrapping, soldering or crimping (if you have to right tools to do it nice), replacing some wires, etc. This is to make any harness reliable again after 20 years. If you extend the harness it is a lot more work than it looks, prone to error, and definitely not worth it, IMHO.
Also, get a harness as close to the body style of the receiving car, engine type, and trans type as possible. If you have an 89 its dicey, because there were changes throughout that model year. It is critical that the ECU and Harness match, preferably from the same car. If not check all the connectors, starting with those to the ECU.
I didn't run into heater line problems because I used the piping from the original motor, not the JDM. If you go backwards - you're kidding about cooling and heat being mixed up, right? That wouldn't happen. IDK if the coolant could run in reverse, but I can imagine lots of ways it might not work and make a mess. Why not run a longer hose and get the direction right?