Thanks again to the geniuses here on the forum, we have the wiring more or less sorted. I thought I would add a follow up message, in case anyone else runs into the same mystery that we did.
The magical keyed 12V pink wire was right was right were Elcam and Texas82GP said it would be. On a gas engine, the pink wire feeds the distributor. On a diesel engine, the pink wire feeds the injector pump. Either way, it is a 10ish gauge wire that supplies 12 volts when the key is on.
The "brake switch" wire was in the main vehicle harness. It is a 14ish gauge green wire and it works exactly the way 81Cutlass explained. With the key on, you will see 12V. When the brake pedal is pressed, the circuit opens.
I don't have a solid answer on the brown alternator indicator wire just yet. I think the LS alternator has everything it needs, but I won't know for certain that its charging until we get a volt meter on it with the engine running.