Bad rom after making changes with FF3usME 6.7

So you're saying you have not applied any patches at all then? Just to make real sure its not that, since battle crashes are usually always associated with a conflicting (or not applied correctly) patch in my experience.

What does the ROM informations window say there in USME when you open the ROM?

Are you getting any errors upon saving in USME, and/or does anything seem messed up in there, like dialog bytes being -11582521 bytes or any other tell-tale signs of corruption?

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What I would do if you are not able to solve this, is re-insert large chunks of binary data from a backup ROM that still works, little by little until it works again. That way you can hopefully isolate the address the problem is happening in and try and fix it - just make sure to make a backup of the messed up ROM first before doing that...
I would start with copying back whole banks like C2, C3 etc. then narrow it down further. That's just me though, there's probably a less tedious way, but I've saved my ROM by doing this before.

I can't stress enough how important it is to make backups all the time!