ZPS File Format

PowerPanda, you never tried the CV to C3 hex grab I prepared for you in this thread about selective bug fixes.  You should give it a shot on a copy of your project and see if it works; it should transfer all of the combat fixes without any event or text meddling.

If you don't want to do that, you have a few other options: if the patches in the compilation haven't been moved (not sure if it's documented, doesn't seem to be in that thread), you can create corresponding anti-patches for them and remove them.  You apply the CV compilation to a vanilla FF6, then the event antipatches, and then make a new patch of the compilation minus the conflicting changes and apply that to a copy of your project.

As for patch file formats, I think a few of the other rom hacking communities are venturing away from IPS.  For instance, the super mario hackers use a BPS file format which checks if the rom you're patching matches the rom the patch actually wants... if they don't, it doesn't patch the file.  Some of the gameboy advance hackers use another different patch format too, UPS file format (applied by a program called NUPS if I recall correctly).  Not sure what the difference is there, though.