Originally Posted by Capt. Obvious!
I have the pin-out, (pin 72 and 59) I don't know for sure what the voltage should be. I read somewhere it should be battery voltage on the red wire, 9v on one of the others (blue iirc) and zero on the last one (which I have). But I cant find where I read it again.
You haven't mentioned checking the charging circuit fuse - fuse 10 - but I'll put it out there anyway.
A description of the connector's wire functions from Ford:
Battery Output Terminal (B+) Circuit 30-BA6 (RED)
The generator output is supplied through the battery positive output (B+) terminal on the rear of the generator to the battery and electrical system.
A Circuit 30-BA10 (RED)
The A circuit is used to sense battery voltage. This circuit is also used to supply current to the generator field (rotor) and to turn on the voltage regulator which determines generator output. It is also used to turn the charging system warning indicator on if there is a fault in the charging system operation.
Circuit 5-EB6 (BLUE)
This is the generator communication (GEN COM) circuit. The PCM determines the optimal voltage setpoint for the charging system and communicates this information to the voltage regulator via the GEN COM circuit.
Circuit 4-EB6 (GREY)
The generator monitor (GEN MON) circuit communicates the generator load and error conditions to the PCM."
I'd be replacing the PCM as a last resort; the rebuild kit you referenced wil be cheaper and easier to try first and an intermittent or faulty VR is more likely. (btw, the above wire colours reference the 2003 model year - the Duratec cars were wired a bit differently and a big 175A fusible link was added to the battery output circuit.)
If you need the diagnostic procedure/pinpoint test mentioned earlier, pm me. It's not that helpful in your odd situation though; once you isolate the alternator as the source of a problem, the instructions are to simply replace it. Ford considers it a non-serviceable sealed unit so it doesn't go into any detail about VR testing.