Ok, I've made a step in the right direction I think. Here is what I did:
This is using FoC 1.1 with the 64x patch.
-install AotR 2.05, then install the 2.05 patch afterwards as you normally would. Be sure to copy "GRAPHICDETAILS.xml" from your FoC XML folder (in the data folder) and overwrite the one in the AotR 2.05's XML folder.
-Next create a empty folder and install AotR 2.50 Open Beta to that.
-open the folder you have AotR 2.50 in and delete the data folder, then click mods, Aotr 2.05, then XML folder, find and delete the AI folder there.
-cut and paste the remaining files over your AotR 2.05 installed in the FoC mod folder.
-open the AotR 2.05 data folder and then go to the XML folder, cut the AI folder and paste it in the AotR data folder.
That's how I got the 2.05 AI to work with 2.50. Now can someone tell me which file I need to go to so I can enable the third faction/Black Sun Pirates?
I'll keep tinkering with this and see if I can add bits and pieces of the AI files from 2.50 and maybe single out what is causing the AI to go passive.
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Edit: So I've been digging around, one odd thing I noticed was the number of files that are in 2.50 that are actually older than files in 2.05, so I didn't overwrite the newer files with the older. Also I noticed that copying the files from the 2.50 XML folder (not the subfolders) seems to make the AI horribly passive, so it's one or a group of those files.