Brandybuck: I know I'm late, but just got started with GOG Fallout 4. First off, I see no reason to insult Todd Howard over this. Grow up.

Second, I had bad mod problems, and followed them with one simple trick. A trick I do not see in the original post:

Add the following to the fallout.ini and under [ARCHIVE] section:

bInvalidateOlderFiles=1

I use Mod Organizer 2, and even though it is supposed to do this, the game STILL needs this in the ini file. In my case some mods worked and others didn't. After I add that, everything is working fine.