Try using Character Respecialization instead. (and Character Respecialization -Console Addon too, if you want). Also, if you are having problems with Improved Atmosphere, you can always just delete the changes that you don't want before you put IA in override. It's modular and has a very detailed description of every folder and what changes they make. I personally don't use any of the custom items or NPC armor changes, but keep the rest. It's a great mod if you only install the changes that you want in your game.