Zone of the Enders and related material, AFAIK, is set on Jupiter (guess that would give us a start for that section...)
Olympus (the artificial island-slash-mega city where "Appleseed" happens) is the size of England (
http://appleseed.wikia.com/wiki/Olympus)... maybe make Mega-Primus the (much smaller) Scotland to Olympus' England?
As for S.E.L.F.: maybe make it part of a semi-alliance of radical groups that support Artificial Intelligence (such as Corpore Metal and the First Church of Christ Computer Programmer from "Paranoia")? Name for this alliance... the "Transcendents" (or "Machine Transcendents")?
Thinking that AEGIS obtains a good chunk of cash from three mega-corporations that it has created to obtain funding, which are MarSec, Megapol and Solmine. Solmine is the relatively smallest of the corps, in charge of mining, refining and selling elements like Elerium, Alenium, Zrbite and other miscellaneous "alien alloys" (like Vibranium, in small amounts). Headquarters are on Mega-Primus with secondary HQ (and its biggest mine within the Sol System) on the Cydonia region of Mars. Other mines are located on other planets throughout the galaxy.
MarSec and Megapol are both corporations that sell weapons, gear and provide for-hire security. The difference is that MarSec provides its security services off-planet and the gear it sells is legally classified as "military-grade" while Megapol provides its security services on planet Earth and the gear it sells is legally classified as "civilian" or "police"-grade (although the former and the latter two are on opposite sides of a veeeerrrryyy thin line....).
Was thinking that on The Line Megapol is not the police for Mega-Primus per se, but they have a very strong alliance and as such blowing away Mega-Primus cops will net you about a 50/50 chance of ticking off X-COM.
The idea of MarSec being a X-COM division is kind of a shout-out to the fanfic "Terra From The Deep" (Oldie X-COM/Stargate crossover).