Pin 1 is the alt output voltage read by PCM and pin 2 is the 60 cycle variable duty cycle PWM signal sent to alt that varies; as it goes up and down the charging does too coming back out of alt. The alt has to have that PWM coming in to charge properly. Meaning the alt is computer controlled. Pin 3 is battery volts off fuse.
Thinking there used to be an oldschool constant charge regulator made for them that bypasses all that but not sure which one to ask for, earlier Ford stuff. The alt is a small Motorcraft 6G type.