File affected by Mods are all located in sub-folders of the game installation path (aka. NOTE that these strings are also found as part of disabled debug code, at offset range: 0x156BA82-156BF38. Enemy Within -> The same as for 'Enemy Unknown'.
PatcherGUI (as of v5.2), part of the mod UPK Utils, includes options to 'Enable INI loading' and 'disable phoning home' for you. Even if all you desire is to install mods and play the game, there are some things you need to understand about the current state of the modding process. Take heart though, Long War is balanced around winning some and losing some. It's intended for those who have to deal with this manually.