1) Would it be possible to set something up where a user preference can be stored? Particularly I'm thinking about the toggle for indexing. I used to turn it on occasionally - but then more and more and now all the time. I don't know how hard that would be to implement at this stage but I just wanted to throw it out there.
User preferences isn't really a planned feature per se besides the config files. In particular, the indexing thing I consider a little dodgy to begin with since the indexes don't actually look at what data is there, they just number the items in the menu from 1 all the way up. So if the menu has, say a "(none)" thrown in there at the beginning, they'll all be off by 1. Or if the menu only shows a certain subsection of the list (like I think the actor starting equipment menus do) then the indexes will definitely be incorrect.
That said, you can accomplish what you're attempting with the config files (and a lot of patience). What you would do is replace each entry of the form
###: Data
with something of the form
###: ###: Data
So for example instead of
25: Explosion sound
you'd have
25: 25: Explosion sound
The program will understand that the first 25: is a numerical index and that the rest is just text, but you'll have your item indexed! Sadly this technique won't work for things that are read directly from the rom like item names, but it will help for things like events, placements, npcs, etc. whatever has a config file for you to change in such a manner.
At the moment I am removing my shortcuts to all editors beside yours; but if you know any offhand that will/will not work let me know. :)
Honestly I haven't had much success with any of the other editors that are out there for one reason or another (part of the motivation for working on this to begin with) so I'm probably not the one to ask, sorry.
- Also, keep up the great work!! 
Of course! Although I'm taking a small breather and it may be some time before the next update due to now having to convert back over from using those image files to actually reading the tile sprites from the rom. On the up side though the file size should be quite a bit smaller in future due to that.
Note: I just came on this : http://slickproductions.org/forum/index.php?topic=144.msg1059#msg1059
- Congrats on having made it so far! 
There's a blast from the past! Boy what a journey it's been...