Pony Fantasy VI Remake

Wow shite, yes that is a lot of changed data. I didn't think it would be this much from all what you've done. I'm aware of the programs altering & shifting large chunks of data, but damn... Well, like I was saying earlier, try for instance to inject the whole clean C4 bank bank in, you'll see in the report there the changed to C4:
from 041D78 (this is C4/1D70)
to
047DB1 (the end of changes in C4)

So basically try injecting the whole clean C4 bank back and try it out, if it still glitches, it's not that and try another...
This is hella ghetto way to do it and I'm almost embarrassed to recommend doing this, but when you don't know what or where exactly to look, it's the only way I can think of and has saved my ass countless times

I'm not sure looking at this log where to start though, but I know doing this technique I could most likely find out the general area or bank once that freeze no longer happens really fast, then narrow it down bit by bit.
I guess I'd start by injecting back the whole E bank (E00000-EFFFFF), and like I said C4 bank.

Once you know which offset(s) is causing this, you can go about tackling it much much easier. ...Unless there has been tons of corruption beyond what is rationally fixable... I mean, everything can be fixed back up to working, but hopefully it won't knock off any of your work in the process.