Proposal:
How Robert Kirkland faked his death.
When Jane and the CBI team last heard from or of Kirkland, he was going away for due processing... And Jane had (apparently) dismissed him as a suspect upon hearing his story.

Then Kirkland got convicted, and sent to prison.
This interlude may be hard to catch, as it is only hinted at:
When we see him in the next scene, at the end of the episode, he's dressed and chained for prison.
And this is where the Tyger Tyger crew took over, and got him shot.
Homocidal prisoners shot while trying to escape, en route to prison, may not cause that much of a ruckus in the media. And the Tyger Tyger crew would likely do what they could to hush down the case, by getting it processed by the right people. So Jane and CBI team may not have heard anything of it, when Jane calls his 5 suspect to meet him at the house.

Essentially, all that Kirkland needed to pull this scam, was someone to aid in the illusion part of his getting shot to death.
My main suspect: the driver, whose gun was used, and who was to call it in, after Reed Smith had safely left the scene of the shooting.
Supposedly, the driver had got a body stashed and ready to replace Kirklands, and might even proceed to blow away the face from behind, making identification attempts difficult.

Kirkland pulls off his prisondress and the bulletproof vest under it, and is driven to a secure location. I do expect he himself ordered the hit and timing, mind.
Probably even ordered a good and dependable shot to do it - through his RJ contacts with the Tyger Tyger crew. He knows exactly how they will handle procedure to cause the least possible ruckus, and can as thus boldly suggest to Smith that he just shoot him point blank, where he stands. A trained pro like Smith would never do so, and Kirkland knows it.

It is not crucial for this hoax whether Jane ever hear of it or not, but only that the Tyger Tyger crew believes Kirkland, the homeland security agent asking dangerous questions, to be dead. And why wouldn't they? After all, Smith did shoot him.
No reason to suspect a bulletproof vest, or that your Tyger Tyger driver is really a Red John pawn, and your victim Red John himself.

[This is a simplified version of theory combo 11112]

Proposal:
The story of Robert Kirklands twin Michael, true or false, is really just a conveniently touching story of how Bob has lost a close relation to Red John, and of why his ideas of revenge are supposedly similar to Janes.

Take note that while Jane is of course trying to extract information from exposed acquaintances of Red John, Kirkland cares nothing for that goal.
Quite the opposite: He is killing them before they can talk of such matters. In other words, he is not at all trying to find or kill Red John. It is a blatant lie, misleading both Jane and the audience from the fact that Kirkland is in fact the only proven serial killer among the suspects.
Apparently Jane bought the touching story of a man seeking bloody vengeance, as he tells Lisbon then and there, that Kirkland is no longer a RJ suspect.
(Of course, Jane may yet actually hold his doubts and be playing patiently for a call of RJs suspected bluffs, such as by consciously giving an unlikely suspect the public 'honor' of being declared RJ, thereby shaming RJ into action, once more.)

Also take note that the tool Kirkland is using as a finger clipper in that scene, is the same kind of tool Lorelei was holding and getting ready to use when RJ ordered her to take of two of Janes fingers.

[This is a simplified version of theory combo 11112]

Proposal:
Robert Kirkland got a major face change operation done
- sometime before Jane joined the CBI
(we see him with his familiar face at that time, in episode #100: Red Dawn)

That is why he's seeking out people who knew him before and asks them if they recognize his face, now that he's been moving around in public.
(If you look at season 2, episode 8, you will see Minelli go to meet what looks like agent Kirkland at the gates of the CBI parking lot, right after Minellis 'horse's assery' speech, once he's talked a bit with Lisbon. It is easy to overlook, and the blurred and distant scene is probably suggesting the level of cautious discretion with which Kirkland let his appearance be seen, back in those bygone days.)

Take note, that in spite of Kirklands claim to be searching for RJ, he never shows up at the CBI to interrogate Lorelei. He only showed up at the CBI when Lorelie was no longer there, and thus can't threaten to identify him as RJ. [except if she gets caught again, or talks] Only once she kills an old helper of RJ, he then gets personally involved in the manhunt for her.

[This is a simplified version of theory combo 11112]

btw
what has happened to Rigsby's freaky ex girlfriend
mother to his son

another Tyger Tyger member defo

Take a look at Kevin Corrigan's Twitter profile photo.

Most importantly look closely at the colour of his hair. Front.

If that isn't Red John, then there is no justice in this world.

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.

Just to add one more important observation to my theory 11376

RJ's victims have mostly been women (when he started killing) - in other words, when he was younger. At this stage he was possibly still unable to control the urges guiding him (until he started channeling his 'tendencies' - possibly after spending time with Mr Stiles: into far greater things than simply killing - a criminal empire)

When women are victims of serials (his earlier victims) one usually pulls up a mommy issue. Kirkland has serious mommy issues.

Mother killed herself to escape a brutal marriage, leaving the twins behind to take all the cruelty and pain alone. In Bob's mind his mother abandoned them, leaving them to take a world of emotional and physical hurt from a sadistic father.

'I won't leave you'....said rather sarcastically as Lennon is dying.

Could this not be the ideal kick off for a young RJ? Those smiley faces have always come across as 'child like'. A crying child's face trying to cover the tears with a 'fake smile' - exactly how a young person would feel after a mom's suicide, 'perceived abandonment' to a life of pain with an almost satanic father.

So mom's suicide is Bob's emotional trigger. (How did she kill herself? Perhaps she slashed her wrists with a linoleum floor cutter - which would finally explain to me why RJ uses such a weapon.....it's a household item from a father's garage type of weapon IMHO)

RJ is born.
Finds his way to visualize
Starts killing women (and others), and signing his scenes with the 'child's crying/smiling face'.
Brett Stiles sees huge potential - but needs Bob to channel that sociopathic potential in a way that is bigger, better. Eventually TT is born.

Maybe?

Anyway, Kirkland is also the only suspect who has given us the 'mommy suicide' story - what a trigger for the dawn of RJ.