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I bought a new alternator and harness, none of the colors on the alternator seem to match up. The larger loop which is I believe red on the harness is black on the alternator (I think, I'm at work right now and going by memory). Anyway is there a way to tell which wire goes where, as the colors don't seem to relate.
 

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Do you have an multimeter or a battery powered test light? Can you post a picture of your repro harness on 'Stangnet?
 

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Did you get the correct harness? The '65 GT harness I know for sure is different.

If you have a multimeter, using the resistance scale, make sure that the FLD lead on the alternator goes to the "F" terminal on the regulator. The STA lead on the alt goes to the "S" terminal on the regulator. And the BATT lead should go to the (+) side of the solenoid and to the "A+" terminal on the regulator.
 
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