You might already know about them, but I've run across a couple of issues with the mod that I wanted to let you know about:
First, in the part of the game where you first meet Aeris and are prompted by her to wait, fight, run, etc, the cursor isn't lined up with those options, and when those options are displayed it acts a bit funny, as each option will show up one line at a time, and you have to press 'OK' after each one to show them all.
Second, I've noticed that when you save a game, just after picking the save slot and confirming the dialog box that asks "Are you sure you want to save" another red/pink-ish colored box comes up after that says "Saved." In the un-modded game, that "Saved" dialog only lasts for a split second, and you can 'Cancel' out of it and resume playing or quit or whatever. But with the mod, that red/pink-ish "Saved" box stays there for around 3 seconds regardless of pressing 'Cancel' and you just have to wait for it to go away before you can back out of the menu and continue playing, etc. It's not really a big deal, but I was just wondering if that was done deliberately for some reason, or is it just some kind of side effect from some of the modifications made to the save screen for some reason?