Time to remove and repair, possibly replace, under dash harness
Alrighty, I have my replacement wires, I'm waiting for my terminals, and I have a plan of action.
Clearly what happened is my charging circuit overheated, for whatever reason, and damaged the red and black wires and some of the surrounding wires. The damage extends from the bulkhead to the ammeter connectors (which have been bypassed).
The branches of the harness look good so those will be left alone.
I am only going to repair what is necessary and get this harness back in the car. It was actually pretty easy to remove and I think it will be pretty easy to reinstall as well.
My plan is to trace each damaged wire as far back from the bulkhead as the damage goes, splice in a new wire and run the new wire to the bulkhead connector with a new terminal.
All of the wires running to the bulkhead will be removed, inspected, cleaned and repaired where necessary.
I'll post some progress pics over the weekend.
Thanks everybody!