A suggestion: offer a Toal Conversion Mod Starter Pack as an alternative to a separata installation (it lets you haveit as a FLMM mod subdirectory, which you can edit and activate/deactivate as a mod, leaving FL directory untouched).
A question/ request: when you'll come to the NPC part, could you, please, highlight ALL the .inis that require changes / new entries when faction itself is edited/ created? Sure thing if it covers your knowledge area.