Have you done a game cache verify?
I would also delete Falout4.ini and Fallout4prefs.ini here: C:\...........\Documents\My Games\Fallout4
ALso delete this directory: C:\Users\
First thing you have to understand, there is no Editor for this game to make mods with, yet. It will release in early 2016. Until then, any mod you use is suspect and will more than likely cause problems as they are made with tools that are not designed for this game engine version. For sure, your saves are in some real danger, so I hoped you created forked saves before you installed the mods.
Because of this, I won't put any mods on my game until the editor is out and mods are produced on it. Texture replacers may be OK to use now.
I've directly put my saves away ^^ And the cache verify was useless to. i'll try to delete the others files and i'll say you after. Thx