OK. Using several of the excellent tutorials here, i have assembled the following evil plan.

I wish to create an MP clan server/mod where the clan is a faction (sort of) and control a few bases throughout the universe.
Using the "close friends" trick, i want to create the empty clan faction which will be allied tightly with another of the more inaccessible (hard-coded) factions, perhaps the Order or the Nomads. Tweak the empathy settings so that the ally hates everyone and hates them more for killing anyone, (aka- no making friends with them). Then i will change the alliance quality of some gloomy bases like Ithaca Reseach or create new ones if nescessary, to be run by the ally so that only friendly players can land there. Alter the available ships, loadouts and commodities accordingly. The trick to allying the clan members to the decidedly unfriendly Ally can be done by using a special copy of the MP player init file for the annointed members. With the rep/empathy adjusted for certain members, only they would be able to land at the special bases and buy special ships/items/etc, and would be tagged with the name of the Ally. I do not wish to be too heavy-handed or create a large mod, using mostly default ships and items, but make cosmetically unique ships and Tags available only to the group that controls & patrols the server.

Before i begin hacking your comments, tips and suggestions are appreciated.