Hi, I never had experience programming an save editor, but there are some things you can do:
Extract your save in .SAV format, on the 3DS you can do that without any problems with any save extractor, even with FBI (Does not count Action Replay save extraction due to different format and stuff)
Start by modifying stuff with an hex editor, or
Extract the save and keep it, modify stuff on the game like names, times, etc. Extract that save again but keep it as second save, compare it on a hex editor, see what changed.
You can always also download a save (like 100% complete) and compare it on a hex editor with yours or a new save file.
If you don't want to inject, and extract the save everytime use an emulator, DeSmuME or NO$GBA will do, make sure you import the save on the emulator first. IIRC DeSmuME had debugging tools, maybe that can help you what's the game modifying on the save. I never used them.