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Hey I did a mustang cobra swap I have a 99 cobra motor run now but Alternator not charger on the cobra Alternator plug has 3 wires going to the plug on the gt/saleen have 2 wires going to the plug so what I did the middle wire I didn't use just the 2 sides wires did I do something wrong which wire to use help anybody
 

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The Cobra alternator will use the 2 outside wires. Pin 1 is a green with red stripe wire that goes to the dash and pin 3 is a yellow with white stripe wire that turns on the field coil. If you aren't getting 12 volts to pin 3, the alternator will not put out any voltage to charge the battery.
 
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