These saves are awesome, however I did notice an issue (and there's probably more).
On Male Alear's "Manual 3" save, not a single character has any additional proficiencies unlocked despite having max bond with every Emblem. I assume this is something to do with you having used cheats to...
1) Extract the desired game text file using UABEA (the bytes.bundle of your choosing)
2) Grab the "MSBT Editor" tool from GameBanana (can't link it here because gbatemp)
3) Load up the extracted .bytes file and edit away
4) Repack using UABEA