Clean Masters won't clean masters that your plugin has any reference to, you'll need to check for them. As for the rest, what? lStewieAl is right, instead of tinkering with all this bullshit in MO2 you just move the .NAM files somewhere else.
The new design it's great for mobile platforms. But it's awful for PCs. The old one is better for that. And I'm sure more people visit Nexus on a PCs than on a mobile.