coil on plug conversion??

i just got a 2000 gt motor. i have the engine wiring harness from the car also with the cops. i had it hooked up for the most part and it ran but like ****. there were a few connectors i couldnt figure out where they plug into. should i just put my old stuff back on?
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figured out you have to use the whole harness. i didnt have the part that connects to the trans and that was where my exctra plugs were at. i already started putting the old stuff back on when i noticed this, just gonna save that for another day.