I just joined and read this thread through from your original query about poor battery life in accessory mode. Everyone who posted addressed my concerns, and then some, quite well (and to reiterate, NEVER pull a circuit while the car is running...bye bye alt diodes). ANYWAY, here's my background and spin:
I own my 3rd and 4th Mustangs, a 65 fastback and 91 GT Ragtop, having owned another 65 fb and a 68 GT/CS some 20 years ago. Now, I have also seen the exact set of circumstances in all years of cars due to one OTHER factor: hick wiring.
What I am suggesting is the liklihood some of your leads are fused within the insulation due to current or previously "hot wired" circuits (foil wrapping fuses). If this is the case, the circuit only goes to ground when the car is on or in acc.
In the former case, the alternator is compensating for the draw to ground. BUT, a small dead short will eventually kill your alternator just as if you pulled the battery cable. ANYWAY, I am positive you have a short that only exists when the key is on, otherwise your battery would die overnight.
Startby re-fusing the entire panel using the EXACT rated fuses listed in the manual. Trouble shoot all circuits that burn...and don't be surprised if they are all key-switched (eg acc).
Good luck
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