Here is my current spreadsheet documenting the format of the individual three save files (save_0.bin, save_1, save_2.bin) after they're decrypted:
https://docs.google.com/spreadsheets/d/18NByL9tgEw7TDYmd5hSnWnxMu1N5gacuQwRzmeCa3Tk/edit?usp=sharingYellow = unsure but is my current guess as to its meaning based on clues.
Red = unknown, but usually have some other context.
I need to get a Dropbox or MEGA account so I can post my save files online so you can take a look if you want.
I still don't have a way to
modify the save files, though. It's really tedious to do this, because I have to do exactly one tiny thing in the game, copy the save to another slot, load the copy, and repeat, until all three files are filled. Then I have to turn off my 3DS, put the SD card into my PC, copy the save file off, decrypt it, analyze the saves, and put the SD card back. Because you have to turn off the 3DS in order to safely remove the SD card, that removes the Gateway hack from RAM, meaning I have to re-exploit it. I then load the game and have to delete save slots 1 and 2, copy slot 3 to 1, and finally delete slot 3. Then I can load the game and make one change to slot 1 and start this process over.
It's really, really slow-going. I just got access to the second room of the graveyard passageway to Sanctuary, to give you an idea. I'm not playing with glitches this time, because I wanted to compare the event flags and see what the differences were between Power Glove Skip and normal play.