2 Silly Patches

Would using a tile editor like Tile Molester also cause problems for editing player sprites, or would using those tools be preferrable for graphic work?

What I would do is use FF3se for the graphics then copy with YY-CHR the tiles changed (Locke portrait and sprite only). There is no pointer involved for those (there are but they are not touched). For dialogues you can't do much.

while we are in the argument... what banks/pointers are changed when you deal with FF3SE?

See ips report above or better save with FF3se, make a patch and check the report.