I have only seen up to Season 5, but it seems clear to me. I can't recall some exact episodes or details off the top of my head, but in the episode where Jane is taken hostage by college students, who killed a classmate and made it look like it was Red John, a suspect was "Grady Ship". Jane goes into the old motel to investigate and is taken hostage to be in a film where he is "sacrificed" to Red John. Red John comes to his "rescue" and shoots his captors for making a "cheap imitation of his work". He is masked, but pay close attention to Red John's mannerisms, body language etc. First clue.
Second, is in an episode early in Season 5, a flash back episode to back when Jane came to work with the CBI, Alexa Shultz calls Lisbon from a limo, and asks to be kept in the loop about Jane's activities after he has been taken on officially as a consultant, she says "It's always good to have a friend in the FBI", which I believe is a quite obvious hint to confirm Jane's suspicion of their being a RJ disciple in the FBI. After she hangs up there is a quick scene where Kirkland is the seat across from her, he says thankyou, Like I said, I've only seen to episode 5 so I'm not sure what has panned out past there, but at this point I believe Alexa is the RJ disciple.
In Season 5 Episode 8, When Jane breaks Lorelai out of prison, Kirkland comes into the storyline again, I believe because he wanted in on the investigation and planned to kill Lorelai when he found her to silence her.. I noted he is always wearing a red/maroon tie. When he first appears and is speaking with Lisbon in a low voice, he sounds very similar to Red John, he could easily manipulate his voice into the higher pitch recognised as Red John's. In this episode Jane passes Kirkland in the hall at CBI and Kirkland says Hi Jane and Jane responds "Do I know you?" Kirkland replies "No, but I know you" and choofs off. Later on, after Lorelai finds out Jane staged his own kidnapping by her, she is beating him up in the motel room and she says she's surprised Jane and Red John didn't become life long friends the moment they shook hands. All this put together I think Kirkland is the most likely option, the scene where Jane has five suspects at gunpoint I believe is a conspiracy as was one theory. Also, if you go back and watch those five's body language etc through the series, watch closely their build, voice, mannerisms etc, and compare it to when you actually see Red John in the Grady Ship episode, I think Kirkland is more likely.
