One question (for the time being anyway): Are the Weapon graphics still in 3BPP?
Seems you figured it out already. ;) The game uses the same graphics loader for summons and weapons, so I had to set up a 4bpp version of the weapons graphics at the end. As long as you copy your changes over to that one everything should work.
My reasoning:
1. It's actually easier to just rewrite the subroutine that shovels graphics into VRAM than to try and work in a jump to brand new one. That always got me into trouble somehow.
2. My goal is to in the end have everything in 16-color mode, so doing it this way means taking care of stuff that would have to be done anyway.
This is very impressive! Especially since graphics code totally stumps me. 
It's really not that hard. Once you've rewritten one you kinda know how they all work.
Holymoly, this works with my project?!
That might be the best news ever!
It KINDA works with your project...
The chocobo was invisible and Old Trees were messed up. The deal is this:
The basic formula stays the same:
[100000] Monster Graphics 1
[108000] Monster Graphics 2
[110000] Monster Graphics 3
[118000] Monster Graphics 4
[11A000] Zeromus Transformed Graphics
[120000] Summoned Monster Graphics
Monster Graphics 1, 2, 3 used to fill an entire bank. As a result not all graphics fit in them anymore. The Leftovers now have their own new bank at the end:
[128000] Monster Graphics Leftovers
Enemy Palette Data is at 11E000. It also follows the original formula: 1. is the Imp. 2. is the Basilisk, etc.
(It's really the original routine with an ASL A to jump 16 colors from palette to palette instead of 8...)
The point being: If you've already familiarized yourself with how and where the game loads stuff it shouldn't be hard to just adapt your changes. Things still work the same way, basically everything has simply been transplanted elsewhere.