That black wire goes absolutely nowhere. I really have no idea why Ford put it in there. Seems kinda ********. Maybe they didn't want to risk water getting through the open hole in the connector? Of course, they could've just used a two wire plug and alternator but then that would cost extra money... *sigh*
Oh, and one of the diodes in your diode pack went out. If you rev the engine high enough, it causes an avalanche in the diode and it conducts, letting the light go out. You need to get your alternator rebuilt (the diodes are pretty easy to replace if you have the correct tools). This will cost much less than a new alternator, which probably won't last very long either.