If you've made exe edits then your mod won't boot.
You need to keep the map file names exactly the same in order for that to work iirc.
I also am unaware if you can edit graphics or not, I'm pretty sure that I'm one of if not the only person who has dabbled with the RetroArch build at all.
You'll pretty much have to either make it so that there are no exe edits, or use CSE2's Wii build instead.