NoobRandomizer

So i basically worked on a randomizer nuzlocke challenge for Pokemon Y. I also managed to randomize Starters and Encounters but no TrainerPKM. I know the Romfs files which i needed to copy into the A folder, those were 038, 039 and 040, although i copied them the TrainerPKM did not change at all. I am using PK3DS. I would appreciate any kind of help, and i would like you to pardon my bad english.