Edited Fire Emblem Awakening rom doesn't open or download on 2DS properly.

[JohnIsAnIdiot]

I have extracted a Fire Emblem Awakening rom and have been trying to apply a mod (specifically Mangs' Awakening CMU) with the edited romfs folder, however, when I compile it all together, the rom either:
- doesn't download
- does download but the banner is all messed up (like it doesn't have the games logo but does have the two Falchion) but won't open
- isn't patched at all, just the base game in it's entirety.
Anyone know how to fix this?

I've tried about 6 different roms.