This one is probably the best to go with for now:
http://slickproductions.org/forum/index.php?topic=2230.0
It has all the bug fixes and more than this Improvement Project, and none of the 'extras'. Unless it's those extras that you are interested in.
I'll agree with Nattak. CV was apparently able to go where I could not; DO, what I could not. I suggest you go with his patch, as I'm pretty much done with this one. I was frustrated by my lack of ability needed to get this done right. I'm just glad
someone was able to make a mega-fix and get it to work!
I've attached an archive with my script translation to a post in his thread - it includes the Opera timing fixes I was working on. Hopefully they'll be useful to him.
If there are any extras in my patch that you wanted to use in yours, let me know and I'll make a patch with the changes I made. Most of my changes can be done in FF6usME, and it sounds like he was able to optimize my Phantom Train fix, but still. I'll help how I can.
EDIT: What the hey. I'll put the archive here, too. I had to expand the ROM in FF6usME to get it to fit, so if there's a better way to insert it that doesn't break everything, knock yourself out.