Check C:\Users\(user name)\Documents\My Games\GalCiv3\Factions, and look for a *.faction file bearing the name (faction name)_(some alphanumeric characters).
Be advised that as far as I know, no member of the community knows how to read or edit *.faction files without using the in-game editor. As such, if you want to edit a custom faction, you have to create the faction "from scratch," unless editing the number of points available for custom faction creation will allow you to do what you want to do (in which case, edit GalCiv3GlobalDefs; look for CustomFactionTraitPoints and CustomFactionAbilityPoints, with the former being the points for things like Dense and the latter being for the things like Starfaring).
