Under dash electrical fire

Update: I finish reinstalling the repaired harness and added a 60A breaker at the firewall feed. I ran the car for about an hour and it smelled like someone was cooking something somewhere. No smoke thank goodness! I felt the repaired harness and it was cool as a cucumber. Checked the battery and it was what was cooking (it’s in the trunk). The alternator was very hot and so was the MSD controller. I let the battery cool down for about a half hour and it is still fizzing and hot. But it reads 12.5 volts and the load tester showed the battery to be very strong.

I am going to let everything cool down over night (with the battery terminal disconnected) before I start other trouble shooting. My first theory is the electrical fire must have done something to the alternator or the voltage regulator and one or the other must be putting out too high voltage for the system. This should be an easy thing to test, with the engine running for a few minutes.

Has anyone else found something like this before?