I believe Red John is Ray Haffner on multiple cases. First Haffner appears in the episode the Little Red Book which happens right after Jane gets out of jail from killing Timothy Carter (Red John Imposter) making Jane a little distressed and hurting his focus. The episode placement is perfect since everyone thought Jane killed Red John but since he did not people will think that Red John will not be seen for several more episodes except they slip in Haffner who the audience is not concerned about since Red John is not dead. Also Haffner fits the description of Red John and falls into Jane's trap in the Little Red Book episode making himself look weak compared to Jane. Another reason why Haffner is Red John is because he likes Lisbon which explains why Lisbon was not harmed when Red John took her. Haffner is also known to be a good wiretapper and surveillance expert which shows how Red John is always in Jane's head while Jane is more person to person and lacking in technological skills. Haffner could also be Red John since in Black Winged Redbird the person who visited Sophie Miller ( Jane's psychiatrist) was named Jay Roth. If you changed the J to an R it would be Ray Roth or Red Ray since Roth means red. In addition to everything Haffner has appeared in episodes only with the word Red in the title and is a Former FBI Agent and CBI Supervisory Specialist and currently a private detective and member of Visualize showing that he has strong connections with all of the agencies.