Tzepish, which ROM version did you use for your changes, and did you do it on a fresh copy or a patched one?
I haven't read the whole thread yet, but I felt you deserved a reply (haven't checked the board in awhile).
That patch was made on the 1.0 US FF3 rom, but it is definitely not compatible with all these bug fixes. Basically, either just apply the changes that I mention manually (in a "thanks for the idea!" sort of way), or apply them to a new rom and take a peek at the data and copy them over. :-)
Other things I think would be neat for a general "FF6 Improvement" would be to import the FF6 Advance dialog and monster/item/magic/esper names, and to expand the names for these things to allow for more letters. Note, though, that some of the monster name changes may result in the alphabetical rage patch to list them in the wrong order (no longer alphabetical), but I believe that patch puts all monster IDs in a table that can be modified to change the order.
EDIT: It turns out I should have read the whole thread, as I have more to say!
The biggest bug I've encountered with ff3ed is this: In the dialog editor, if I add too much dialog, the rom becomes corrupted such that the overworld will not load. And, if you wait too long for it to load, your save files are deleted. Nasty.