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With the alternator unplugged and the engine running, one of the wires from the PCM will have a 12 volt reference on it and when plugged in that circuit turns to about a 1.5 volt square wave signal that is used as a feedback from the alternator to the PCM. The other wire at the alternator will show very little voltage when the alternator is unplugged and the engine is running and then turns to about a 10 volt square wave when the alternator is plugged in, this is the command circuit for the PCM to tell the alternator to charge.
Be sure that all of the inputs are correct going into the back of the alternator with the key on.
You will need to check for this square wave from with a lab scope.
If all the inputs are correct, then the new alternator is bad and will need to be replaced.
2003 Jetta left rear window blue plastic part of the