So:
1) I messed up with having the FOOK files overwrite the FWE files? If so, should I go back and reinstall everything?
2) I should sit tight on the weapon and armor images not showing up for now?
I find it extremely helpful to use 7zip or winzip or something similar to maintain archives of various mod versions. This includes ANYTHING that goes into my data folder. I try to get it set up to how it will look after everything is done. (ie: If you take some of the FWE resources from the resources subdirectory and put them in the data directory (ie: optional mods, compatability patches, etc), then do so in this zip file too. ie: The file should have whatever the particular mod would look like in the data folder.
Then, use the fallout mod manager's package functionality to actually install or uninstall. This makes updating, reverting, etc. very easy.
ie: If you were using this, and you accidentally made FOOK overwrite FWE instead of the other way around, you would just "deactivate" each one in the package manager, then reactivate in the proper order.
If you have many mods, and they interact with each other (ie: overwrite each others files, etc), or if you have a different set of mods for a different set of characters (say you are playing a vanilla runthrough, as well as a fully modded runthrough, as well as a runthrough with XFO, etc etc), you can use the package manager to only install the mods (including all textures, sounds, and so on) that you are currently using.