The alternator is ECU controlled. Pin 3 is +12v battery. Pin 1 and 2 are how the ECU controls charging voltage and monitors charging voltage (GEN-MON and GEN-COM). Pin 2 is the PWM signal and is needed for the alt to charge. Pin 1 is the monitor circuit and isn't needed.
Do you have the ability to provide PWM signal to the alternator? If not, it won't work.
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.
American Muscle Late Model Restoration LMR PA Performance Alternator Starter Ford Jeep Dodge Ram Cummins F150
for non-computer control.
HOWEVER.......be aware that that particular alt has flaws and the regulator is one of them, they are flimsy and blow out easy unless you demand a heavy duty version of it. When I rebuild my Focus one I order the Transpo brand F601HD for heavy duty, they kast MUCH longer. The diode plate is well known for vibration cracking of the leads that can pass testing but the alt does not charge right. There is a heavy duty diode plate that stops all that too but has to be soldered in.