As of today, 4.0.4, v1.1 WORKS with Female Toons and Companions, best to use the "Covert Armor" set with this. With the Outfit Designer, you can switch between the naked set with another fully clothed set.
Start launcher, let it patch, THEN running the file replacer, when it finshes close the replacer, then click PLAY.
After I logout I run the restore backup option.
1.1 makes naked your female toon, female companion, and will randomly hide other players tops, while their companions will be nude as well, in most cases.
The only true issue I'm having is that you have to not have anything in the Leg slot of your base outfit in order achieve the full nude look.
God Bless the OP for this awesome mod. A+++ COOKIES FOR EVERYONE!!!