I have several mod files that I have gotten from others on the forum for custom races, as well as faction files (which serve the same purpose but are located in a different directory. From time to time while the game is changing a lot, I tend to reinstall (I have about 60Mbps download from FIOS, so it's not a big issue). But before I reinstall I rename the C:\Users\Bamdorf\Documents\My Games\GalCiv3 file something else, like Galciv3_old. Then remove the program through Steam, and the files in C:\ProgramData\Stardock\Galactic Civilizations III and C:\Program Files (x86)\Steam\SteamApps\common\Galactic Civilizations III. (Or rename the last if you like.)
After reinstalling, I just copy the contents of the mods directory C:\Users\Bamdorf\Documents\My Games\GalCiv3_old\Mods to the new mods directory and I copy the factions directory C:\Users\Bamdorf\Documents\My Games\GalCiv3_old\Factions from old to new in the same fashion.
Haven't had any problem with this procedure and I am closing in on 100 factions. Maybe this wlll hep, good luck in any event.