Final Fantasy VI: The Redemption "Translation"

I don't know how to help you with this specific problem, but I'll tell you what I do with my hack so that problems like this don't arise.

Actually, the reason I started doing it this way is from reading posts about Pandora's Box. They have implemented many fixes and features, some of which people requested to have separate. The PB team said it was too hard to isolate the changes in their ROM for specific features and provide an .ips. I thought about this and decided to compartmentalize my hack before I even started, so if anyone liked a specific part of my hack, I could just give it to them.

For example, I have a separate ips for my font (including menu font and ATB gauge), one for my graphic edits, a few for my separate parts to the dialogue, and an .ips for the small changes that are just easier to make in FF3usME. I also have an .ips for the changes I make to Angelo's restored abilities patch, just small changes like a few esper names, commands, and some classes.

It seems like overkill for one hack, but it keeps everything more organized. If I want to edit my font, I just have to open my clean ROM with my font edits, so I don't accidentally change any other data. When I'm ready for testing, I just apply all of the patches at once, and if I see something I want to change, just go back to the individual patch and make the edits.

It's probably too late for you to do this, but judging from the problems you're having, it might be a good idea to start fresh. I could help you with this if you'd like... try to salvage what you have.