You have what is called a PWM alternator, which can step its output voltage based on a signal supplied from the ECU. Unplugging it should allow it to run in a default output, but you can also pick up a small PWM controller or PWM generator and command it to whatever voltage output you prefer.
This thread should have a lot on information for you:
https://ls1tech.com/forums/conversio...hrow-away.html
Edit: If you are running a factory ECU/tune with your swap, then it is completely normal for the alternator to show a low output state. The ECU will lower the alternator output to improve fuel economy under certain conditions.