Progress update on character modding! Hooray!
First off, no dice on the "adding more characters for a single stage" idea. It's not impossible, but I can't figure it out so far.
On the plus side, turns out adding stages is far easier than I thought. Make a new "map" for your stage, add its data in the game's database, then add a button to access it on common event 208 (stage select). Buttons are added on line 247 and below with a "call event". You want to copy one of the "call event" lines and choose your new stage, as well as the button's coordinates. That's it! So now the limit is how many stage buttons you can fit on the screen I guess.
A word of advice for anyone who wants to try making a character mod: Remember to document the changes your mod makes, since your mod will likely overwrite part of the game's files. That way it'll be easier to fuse mods, and potentially make character packs and stuff.
I'm not an expert though so I don't think I can help beyond this. Good luck!