Matt,curious ?
you mention up top the original 55 amp alternator could not keep up with your system
did you have that one tested prior to the install of the GM one
perhaps the OEM one was simply bad or going bad and dying on you in the beginning
just a alternative point of view not brought up yet ?
if you still have it a solid diagnosis on it could help solve this issue 100%
\
matt
I would create a situation with a separate light bulb to get your charge light to come on (and go out) as it should. I would temporarily bypass the Toyota dash light relay and bulb. I rewired a 6v Ford tractor and used a light bulb to excite the alternator into charging.
Some diagrams and ideas here, although using the GM 10-si alternator:
Ford Tractor 12 Volt Conversion Wiring Diagrams 9N 2N
myfordtractors.com
I installed a GM 1-wire alternator on my '65 FJ45 (with an '83 2F engine) and it was super simple, had 85 amps of current, and was (of course) incredibly easy to wire. If you get desperate, that might be an option.