Got my hybrid system working again!
After pulling the car completely apart, I found this under the dash:
Looks like the white wire in this connector changes colors a few times and is responsible for connecting the fusebox under the hood to the "ignition hold relay". The fuse blew, but not before the wire melted in half and damaged the plug it passes through under the dash. I'm not sure if water got into it, or if it was just a random failure. It could have been that my grid charge harness was responsible for a loose connection on the bypass resistor at the IMA battery, that the fuse was faulty for not failing first, and that this connection was the weak point in the circuit. Really not sure.
Anyway, I bypassed the burnt wire with some extra length and a spade connector.
Some other pictures while I had the car apart:
