FF6: Messing with the final battle lineup

Thanks for that advice, madsiur! I started poking at the save file I had and I have discovered two things:

1. The game really does not like it when you swap Terra in for Celes immediately after leaving Solitary Island and trying to trigger the Tzen event.
2. Adjusting the bits in my OP successfully removed everyone from the party that I intended to remove, which also removed them from the battle order menu before the last battle, but it did still include them in the ending. So, I think that you might be on to something with the "initialized characters" spot in the memory, so I will likely look at that next.