I was wondering if there was a way to make the conetrooper and storm trooper mods compatiable with the brother hood of shadow mod and the upcoming one too. I am able to wear the clone and storm trooper uniforms but the soldier replacements do not work.

You want to tie the Brotherhood of Shadow to the Clone and Storm Troopers? Why would you want to do such a thing? It's like tying the prequels to the original trilogy! Or a plague rat to your breakfast! (Reffering to the BoS as the horror in my metaphors. Some of you are just so dense.)

Ok, joking aside just copy over the .utc's from the trooper mods into your Override folder again.