Okay, yeah, so you do need to do everything, in order:
* Clean up the mess in .kobo (which, hopefully, should basically be the .kobo/.adds folder, as well as potentially the .kobo/icons folder and the koreader & kfmon PNGs inside the .kobo folder. You should also have an *empty* .kobo/.kobo folder that you can remove).
* Tweak the config file to prevent nickel from scanning those custom folders.
* Unplug.
* Wait & watch Nickel destroy the icons from the stuff installed in the *right* place.
* When it's done (there's unfortunately no clear signal, except maybe for "the book count in the 'My Books' tile stopped decreasing". Except I've seen that counter sometimes not actually getting refreshed on the Home screen, so, double-check from inside the Library view), plug it back in.
* Reinstall KOReader/Plato.
You're now starting to get my repeated comments about doing it right the first time around, as messing it up gets annoying real quick
.