Your problem is the location of your capital I think. Have you checked the settlement details scroll of Kotais. My guess is that you have something in excess of 40 % minimum distance from capital penalty. Add to that the culture penalty and the general unrest factors.

Keeping Kotais will become a nightmare. It's allways like this with far flung empires. Someone posted that they had conqured most of Africa and Europe in a Carthage campaign but were having troubles keeping some of their most far flung holdings in check. He/She wanted to go conquering in India but the game mechanics simply wouldn't allow it due to the distance and culture penalties.

I had the same problem in my Sabyn campaign when i conquered Hierosolyma and Sidon. They kept rebelling because my capital was still Maryab in southern Arabia. When I moved it to Dumatha I could keep the two cities in check but had to increase the garrisons in southern Egypt and Arabia due to the distance to capital penalties.

The only way to keep a large empire from falling apart is to make the capital the most central city in that empire. Basically equally long distances everywhere. Add happiness buildings and strong garrison you may just be able to keep the most far flung provinces to obtain your victory conditions. The fringes of your empire will be restless though. It's game mechanics, pure and simple. Propably hardcoded to boot.

Increase the size of the garrison and find a good governor or several to keep order. That and move your capital closer. Add plenty of happiness buildings. High level order increasing temples are best. Garrisons second, and game fields last. Apart from that don't have any other advise.

Hope this helps.