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When the a/c is on one of the fans should stay on all the time while the a/c is on.The. Other fan comes on when the car hits the correct temp setting. Sounds like you may have a ground issue. Did this start before or after you installed the headers? May you unbolted a ground from around the head or one that came loose. Are you getting a check engine light also or just a message on the DIC? Trace your steps from what you did prior to when the problem started and you will probably find what it is. If it fixes the problem when you mess with the harness you may have a bad connection or broken wire in that are you can't see due to the wire insulation. Electrical problems are usually not easy to find just be patient. Remember if you turn on the a/c and it doesn't kick on the fan immediately then only one fan is working and the car needs both to keep it cool. Also air pockets in the system will cause problems also so you may need to read up on burping the system.
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