So you cannot edit the CMB files in any way?I can't seem to edit the cmb files from Ocarina of Time 3D. I can view them, just not inject textures or anything. I used N3DSCMBViewer by xdaniel to look at the cmb files.
if the problem is injecting them, what about going the Luma3DS romhack approach?
Putting the modified files in a specific location (folder with Game ID) and then via Luma making the game boot with those files.