Psy, i had some notes i made from before you even started this project. Back then i tried hex editing some preexisting dungeons, and in order to do that i dug deep into that gamefaqs topic for information. You might already have all this information, but i decided to post in here just in case you didn't. I hope this helps you even a tiny little bit:
http://pastebin.com/kWDYtbQe
I remember that it took me like 6 hours to dig this much information from that topic, and that i wasn't 100% sure that i didn't made a mistake when writing it. So while this might help, when in doubt presume that my notes are wrong okay.
edit: Also, once you figure out the rest (like what different values mean on each byte and which offsets are for which dungeons) making an utility to edit dungeons shouldn't be very difficult for you.