I don't know how to fix your issue with copying the gba save to the memory but the save trimmer should ask you if you drag the save file in about the size in kilobytes you wish to resize too
I didn't extract any of my saves when i was doing it since there was no data to backup for me
Injecting gba saves is possible with godmode9 using this guide
and use this to resize gba saves to 32 kbs
https://www.dropbox.com/s/ubqgow5ea2gb1v0/Trim_VBA_SAV_recompiled.zip?dl=0
I'm trying to access it from arm9loaderhax by holding start on boot but it keeps displaying the "Failed to mount CTRNAND" screen instead of loading arm9loaderhax