Here's the thing. "We ain't there." Not tryin to be mean. When you modify from factory, then it's difficult or impossible to follow what you did with wiring changes or / what caused this
TIMING: You may have reversed the pickup wires in your repair???
So far as the harness, this can kick your ***. Some short somewhere starts "meltage" and once several wires are welded/ meltaged/ tied together, then all kinds of stupid stuff happens
There are several circuits in the harness that are NOT very well or at all protected.........except by the fuse link
The blue "ignition run" which provides "key on" power to ANYTHING under the hood such as alternator field, ignition, smog doo dads, and so on. IS NOT FUSED
The alternator "charge" , field wires, and ammeter wires are NOT fused, other than fuse link
I once had a loaner car while my RR was in the shop after some girl rear ended the thing. The loaner, one morning, dropped a diode down inside, stopped the alternator. When I messed with it to see what was wrong, I just stood there "in awe" (and shock pun intended) as the entire underhood harness fizzled, smoked, and burned all the way around, and then..........popped the fuse link