Okay, tonight I was finally able to get over to the shop and examine things in light of your comments. First, it's clearly a three wire alternator. Second, it only has one wire going to it, and it is the large wire that goes straight to the positive side of the starter, where it meets the battery cable. The terminals on the back of the alternator are not marked one or two. The one shown above two is the furthest one from the battery location; a quick check on a buddy's showed the same thing. So I made a short section of wire going from what should be #2 to the battery terminal and started it up. The volt meter in the car was steady at just short of 13 volts, pretty constant the whole time. Then the light thing started it's blink thing again, did it a few times, I shut the car off. I have not run a ground from the engine to the body. I do have grounds running from the body to the frame and from the engine to the frame.
Any guesses? I'm getting closer to bald all the time. Thanks for all the thinking and help.