There are three harnesses when going stand alone. There is a main harness that fits every application, an injector harness, and an ignition harness. The injector amd ignition harness plug into the appropriate plugs on the main harness. The factory injector harness won't plug into the FAST harness.
Keep in mind, a stand alone harness will just run the engine. You will need to wire a few other items, if you remove the factory engine harness.