First of all, I don't have C3C, so this isn't all too informed.
Iraq, Kuwait, Bahrein, Qatar, and Kabul have to go to the US. Not....Sudan.....
Civ being a realist game, this gets a bit hard.
One thing to do would be allow various states to make priveteer-like Terrorist units, which would be like cannons with defense. They wouldn't have national markings, and they'd bombard, but they would also not be capturable and be able to defend and attack directly.
Najaf and Falluja could be given to an Insurgents civ or something, with insurgent nationals in other cities. Most of Afghanistan shouldn't be under the US, but it could be under some terrorist state, as could Waziristan or whatever its called in Pakistan. Palestine could be seperate from Isreal (both of which would obviously have to exist) and have Gaza and Ramallah or something.