Like @Pighead , I am not an electrical expert, but I've been fighting a similar thing, and so in reading on alternators, a couple things have come clear to me.
Try removing the main charge line (if your wiring is still stock it'll be the white/blue that's hooked to the 'B' terminal on the alternator) and use a multimeter to see if there's still voltage at that stud (ensure good ground with your other volt-meter probe). If you're measuring with this wire hooked up you might just be getting a reading of the battery and not what the alt is (or is not) putting out.
Also, I've read where the output voltage should increase with RPMs - i.e. that you might not see anything above ~12.4 at idle and that most charging happens when driving. Point is, hard to test for 'charge voltage' at idle (it's what I've been trying to do, so I'm equally unsure if my alternator is outputting the ~13.5-14V that would be expected if it were providing the battery proper volts to keep it charged).
That's about all I know. Hope to help. Or at least get the conversation going, and someone who knows can educate us both!!