Sure. This is the basic folder structure for the RPX version, which you might want to try again. This is all you need if you're launching from the RetroArch Channel linked in the OP (nothing is needed in the wiiu/apps folder).
sd:/retroarch/config/
sd:/retroarch/cores/
sd:/retroarch/cores/info/
sd:/retroarch/cores/logs/
sd:/retroarch/cores/playlists/
sd:/retroarch/cores/savefiles/
sd:/retroarch/cores/savestates/
sd:/retroarch/cores/system/
sd:/retroarch/database/
sd:/retroarch/database/cursors
sd:/retroarch/database/rdb/
sd:/retroarch/downloads/
sd:/retroarch/filters/
sd:/retroarch/media/
sd:/retroarch/media/xmb/
sd:/retroarch/retroarch.cfg
sd:/retroarch/retroarch-core-options.cfg
If you're launching it from the Homebrew Launcher, just add these:
sd:/wiiu/apps/retroarch/icon.png
sd:/wiiu/apps/retroarch/meta.xml
sd:/wiiu/apps/retroarch/retroarch.rpx
Also I'd highly recommend using only the latest stable version (1.7.8) instead of the latest nightly build as those can be unstable.
I'll reinstall again with 1.7.8 and report my findings.