I fear you discovered the main issue why we stopped working on the final 1.3.
The codes weren't clean and we had a lot of chaos in the mod resulting in various issues that are nearly impossible to fix. This won't be an issue in TPC but unfortunately there isn't much you can do to get the 1.3 GC AI working properly without spending ages on this. Sorry I can't be more helpful:(
Expansion_Factions.xml = Underworld Faction for the FOC Addon
You could try to download the pegasus chronicles and get from there
Factions_Additional.xml = Many other costum factions
then overwrite original Stargates FactionFiles.xml to initiate the 2 new files there.
I guess it wont work by the first try, maybe if you play with it you could add a faction but this is hard to achieve.
Also you can open any GC XML File ( indexed in CampaignFiles.xml ) and search for <AI_Player_Control>
This tag assignes a faction to a player. SandboxHuman is the human player, rest is AI
So if a faction allready exists you can assign any AI to it like for example:
OK. I added <Basic_AI>BasicEmpire</Basic_AI> under freie Jaffa in factions.xml, made sure <AI_Player_Control> Freie_Jaffa, BasicEmpire </AI_Player_Control> was in the replicators campaign of destruction block when playing as rebels, and gave them $800,000 and tons of starting units just in case but it seems to have no effect.. they still don't move from cal mah.
seems like it should work unless like locutus said this is un fixable
also, funny how some ai works like the wraith and asurans in pegasus galaxy GC and Ori in Ori campaign GC