I intended to come back sooner to release more notes, but here I am before 6 months later at least! I have many more notes to share for Pokemon Super Mystery Dungeon, some of which were made easier to make due to (and based off of) the contributions of the people in this thread, thanks to Blue587 and Andibad! Some of their notes were used as a baseline for anticipation and fleshing out things further. I will go through each file with some explanations...
This file was made without actually testing changes in-game and was mainly deciphered through extrapolation, and Abilities are largely not editable. However, ability_data_info.bin manipulates some aspects of Abilities thankfully, leading to softly modifying abilities being possible but very limited. Ability Data Info Notes.txt
For information on the general rules for Dungeons, changing their info on the dungeon selection screen, and altering how they'll operate inside, these (incomplete) notes provide that. Dungeon Data Info Notes.txt
This next one was a big undertaking. It took forever (like 2 weeks?) to get all the Map IDs named and carefully ordered. dungeon_map_data_info.bin handles dungeon scenery, music, environment types, dungeon layouts, etc. Basically the in-dungeon stuff, handling the generation and atmosphere, but not items or traps, I'll get to that in a moment. This file has 533 map ID entries, some of which are left over from Gates to Infinity. The other stuff besides the map ID entries are still somewhat unknown and incomplete. Dungeon Map Data Info Notes.txt
Next file is the experience.bin, which of course handles Pokémon Experience and stats gained via leveling up. A guide is inside on where to find specific levels. Experience Notes.txt
As for Move leveling, grade.bin handles this. Grade Notes.txt
With the help of Andibad's notes, I made some notes for PSMD's act_data_info.bin. It's very incomplete unfortunately and needs a lot more testing and documentation of certain IDs. Act Data Info Notes.txt
But finally, I can now get to the real deal. Huge thanks to Blue587 for me with this and making this possible, I finally have notes for PSMD dungeon_balance.bin. The file handles the meat of what's in and occurs in dungeons such as items, dungeon status, traps, water and lack thereof, Kecleon Shops, Monster Houses, Pokémon, etc, etc. This is pretty incomplete (and has some things that are actually untested, not unknown) but not so much so that you can't make substantial changes. The special generation, chance, and frequency of things in dungeons can be easily edited. But for Pokémon, adding them in and modifying their attributes can be challenging and tedious. To zoom out a bit, these notes DO NOT document the raw dungeon_balance.bin. The dungeons inside must be extracted and decompressed. If you know how to do that, these notes will be usable. Super Mystery Dungeon Balance.txt
Lastly, this an unrelated but a hopefully helpful consolidation of the additional effects moves can have since the chances can be different compared to the main Pokémon series. Bulbapedia doesn't provide info on chances for additional effects for Mystery Dungeon Games. This lists the usual status conditions damaging moves can inflict, either to a foe or yourself, along with their chance (ordered by chance not alphabetically), including critical hits, and interactions with additional effects. This does not include Abilities. This information for the chances was gathered with the help of DreamNexus. Additional Effects.txt
I of course have several other notes in the making, but due to limitations I can't complete certain ones right now. Hope these help!