You can use the wiring harness with any system II boardset. Everything that plugs into the logic boards is the same. You will have to change the wiring for the control harness.
Also keep in mind a few other things:
1. Some system II cabinets have different power supplies/sound boards. Some use the ARIII plus a small +5V supply for logic, and others use a switching power supply and a small audio board. No harness is perfectly plug and play with both power setups.
2. Some of the system II cabinets have different internal geometry. That being the case, you may find that the wiring harness from one may not span the distances required in another.