65amp wiring/trouble shooting

A little more information about "the red wire you asked about." From the factory service manual, starting from the B post on the starter relay - A1B 10R connects to fusible link A1C 16DBL which enters into bulkhead connector J. Then color changes to red A1 D12R on dash side of firewall which is capped off near ammeter. This wire is capped off because its not used with the 60 amp option.
If you see more in the service manual that may cover the two black wires through the grommet, please post.
Because that part of the scheme is not shown (at least in the diagrams I was looking at) I wanted to leave open the possibility that the standard A1B was not reused for some other purpose.

To the two black wires coming out the grommet. They merge into a single thick brown cable that goes right on top of the alternator.
It's possible they are spliced into a junction.
The red wire you asked if it is connected to a fusible link, yes is does. The wire goes from the starter relay into the harness, then it goes into the white connector. Then, it continues as a black or smth wire to a fusible link which ends in the bulkhead connector (you can actually see it between left and middle connector on the bulkhead)
It seems likely this a segment from the standard wiring (as townsend wrote) and is no longer used for any circuits.

Lemme look at your photos next