[Sniped]Also that new load order messed up my Metro 2033 armor mod so now the helmet keeps disappearing and reappearing.
Impossible that the new load order messed anything up, and here is why. I looked at where you have that mod placed in both load orders, it is placed very last in both. In both cases, no other mod could make any changes to it cause nothing was loaded after the mod in both load orders posted
I highly suggest that you start fresh (even deleting the data Fallout 3 folder after you un-install the game), and that you slowly add mods to make sure they work. You could either have a mod that isn't compatible with FWE, or maybe you have files left over from mods that you decided to not use anymore. If you really don't want to do that, then I suggest you can start disabling mods until you find the mod that is preventing FWE menu to show up.
I know people hate to read the read-me's, but it sure does save hours and hours of frustration when you read if the mod is compatible with another mod, and where to place it in the load order. I know that you have 2 night vision mods and I don't know if they are compatible with each other.