I have a small problem with the DK_BulletTime mod that is included in FWE, I somehow managed to bind the hotkey to ESC, but now I can't change the hotkey. When I open the menu to try and change it, the menu instantly closes and doesn't allow me to change anything. If all else fails would it be possible to edit FWE using the G.E.C.K and change the hotkey manually?

Also just noticed that my game CTD's if I try to do any type of save... No idea what would cause this.

Mod settings are saved in your save file. If you want to do a reset (clean save), unload your mods, reload your save, save game, quit and reload with your mods active. Then all settings will be restored to default.
Though I dont quite understand what you mean with the 'menu instantly closes'? So you open up the FWE main menu and then it closes instantly? That can't really happen, since it cant possibly close without you clicking an option.

Regarding your save, you might want to try masterupdating your mod list. Or you might want to check if the save problem happens everywhere or only in a certain area.

you could click the button in the FWE menu that puts all settings back to default?