[patrickt]

I would:

1) Put the two wires back on the VS.

2) Look around as best you can for anything that you hit that, maybe, would be around the manual fan switch. I'm actually having trouble conceptualizing how that fan could even come on by just turning on the ignition switch.

3) Implement Bob's wiring change that eliminates the need for the ignition light.

4) Leave Fuse #3 out of the fuse box. We'll tackle that short last.

5) Start the car, see if you're charging properly (the ignition light is disconnected so don't worry about that), and see if the fan comes on or stays off.