Well, I think I found the answers.
I tried to start the car again today. First time, same as before. Then I started trying to shove my multimeter probes into the battery terminals in order to watch the voltage while I tried to start the car again. This time, the car started up okay.
My conclusion is that the terminals weren't making good contact. My "cleaning" didn't include a good scraping or wire-brushing, and I didn't have any appropriate battery terminal goo handy. These will be addressed soon.
Also, the issue about the extra fuse holder was solved by me happening to look under the passenger seat. I found a couple of extra-heavy-gauge power wires and a couple of RCA stereo pairs. I then looked again at the battery side and found that the wire matched. It was really nicely done, with wire loom that matches the factory style, and it went through a grommet in the firewill (near the brake booster) to look completely stock.
The radio is just stock, but now this is giving me ideas.
In any case, the good thing about the problems I have having is that I've found this forum. On the flip side, I'm now paranoid about my head gaskets (after reading a number of threads here). Hope mine hold out for a while.