Well, after trips to 2 Ford dealerships, Napa, ACDelco and Direct Auto parts, I still have NO idea what that plug is for. A mechanic I know said it's for the battery light on the dashboard. Regardless, I slid it on, and put everything back together. So, for now, the car is running. I am out of time for the day, but tomorrow (or sometime soon) I will refill the transmission res (I took out the driveaxle to make room for the alternator to come out and go in.
So, the new alternator is in, and good for now.