New version uploaded, which handles force allocation better, and should fix that weird situation that your particular save game was in. please add the mod in and try it out. Be aware that you have ~10+k chunks generated in your world, and over the period of about 30 minutes they will all be fully processed and be properly separated into the different factions.
Let me know how you go, but keep in mind the various testing issues I encountered and be aware that there might be some initial period of slow-down due to the huge battles going on. The mod wasn't really intended to have massive uber-worms in the world, and also adding the mod to a 10k chunk world was a challenge in itself, but it should be reasonable smooth now from all my programming upgrades.
The only thing to really keep in mind is the update time required for Repair Turrets..