OK. A lot of questions...
AC: Currently the AC system picks up power from some sort of tap into the harness. It then goes to the AC unit and then takes a separate path though the AC line openings to the compressor and the AC fan. Seems pretty wonky, and I may revisit that for a better, more integrated solution. HBChris said all AC was added by the dealers.. so that's why this so wonky.
Battery Protection: I am not planning to relocate the battery. Part of this is PTSD from the 1967 MGB-GT I had in college. The long run from the batter(ies) under the rear seat in the MG made for chronically difficult starting (didn't help that it was two 6 volt batteries in series, so multiple connections).
However, I'd highly recommend using something to isolate the raw battery line from anything it is powering, especially with the long run through multiple potential abrasion points.. Either a fuse or a relay. On my boat I used some high amperage fuses that are part of the battery terminal (see link), so any short anywhere that draws over 100A isolates the battery. In your case a relay would be similar, although I would fuse each line from the relay output. I'd also consider either putting the battery relay in the back, at the battery, or fusing the battery line at the battery, so if for whatever reason there is a short on that line it will not incinerate your car. While it is probably water under the bridge, There is a huge difference between the starter cable and the rest of the car in terms of amperage. So, while it is a PITA, you may want to isolate the starter power from the car power, since the starter is the only thing that requires a super high average connection to the battery.
The ideal setup, IMO, would have the battery cable, armored in some way, going directly to the starter, then a relay and fuse protected line to the rest of the vehicle B+. This might save wire by hopscotching from the starter to your battery tray distribution block.
Basically think of the battery as an electrical bomb. If any wire connected directly to it shorts, then boom...So the closer to the battery you can protect, the safer everything is...
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