If Ray Haffner is Red John, then why would he pay someone to bug the CBI?  He had permission to be in the CBI office anytime he wanted.

He could have bugged the room himself, so why would Red John run the risk of exposing himself by hiring a private eye to do something he could do himself.  Further, the bugging makes no sense at all any way.  If the private eye were to listen in on the conversations in the CBI, she would put two and two together and realize that the person who hired her to bug the room is the suspect the CBI is hunting. 

Therefore, in my opinion, Red John is not Ray Haffner.