Ammeter Battery overcharge

I went back to your beginning post. I'll assume we are still at no start.
I noticed you stated that nothing hot at switch on works. You stated hazard does work. If hot at all times ( includes hazard ) does work, do headlights work ? If yes, the ignition switch is suspect.
After the ALT' gauge there is a weld splice where the black wire branches to 3 or more connections. One is the side of the fuse box that is hot at all times. Another to headlight switch. Another to ignition switch. If that switch fails nothing beyond it will work. It's slow death could have created resistance and all of the conditions you saw during that period ( screwy charging system, poor idle, and more ).
Now about the aftermarket harness ( M-H or whoever )... A reproduction should be exactly that, Identical to OEM. ( to make it wrong is just sad ). Anything else should be called "custom" or "modified". So sure a mfgr could move the circuits around in the bulkhead connectors for whatever reason but.. only if they provided both inside and outside connectors/harnesses.
And yes the OEM fusible link was red with a yellow rubber id tag. The color of a fusible links casing helps identify it and/or its gauge, like the modern blade type fuses. Lots of sexy colors to be had today. A engineer would draw the wiring diagram with what ever wire color is feeding into that fusible link ( as if it wasn't there ), not the color of the link. In more modern drawings a symbol ( with or without the AWG notation included ) could represent a fuse or fusible link.
You also stated earlier that you had discovered the fault in this aftermarket harness and corrected it early on and you've had no electrical problems since.
I'll say this again, the bulkhead connection is not the only point of failure nor is the madelectrical bypass a cure all.
From what I've read and think I understand, I feel I would find your problem in power distribution under the dash. If not the ignition switch, in the weld splice before it. Until you park it here, that's all the help I've got.