being rooted shouldnt effect the update. and cwm disables ftm, and is also the reason you cant do the ota update. you have to install stock recovery back over it
i know you didnt mention the ota yourself but i figured id throw it in there to be clear, you cant use any method of official update with cwm installed on the phone and root shouldnt have anything to do with your inability to run the updater as long as you havent deleted or modified any of the other files. using the ota while on aa just wont work to my knowledge and if it did manage to install you better believe youre gonna have some issues lol