Actually, MICHAEL Kirkland. He's the thing. The person we've been lead to believe is Robert Kirkland is actually Michael Kirkland.
We know when Michael was "Killed," he was shot by a known Tyger Tyger Head Guy, Reede Smith. The chain of Custody was him and the driver, another TT member.
We know from "Bob" Kirkland told Jane that his brother got involved with Red John and he presumed killed him. That is why Kirkland supposedly got involve in the hunt for RJ.
Instead, RJ has been keeping his innocent brother in captivity all these years. Using BK's credentials and avenging his murder as motive he packed every background check, where MK certainly could not.
Also, why was TT so intent on killing Reede Smith? Because he's the only person on Earth that knows "Bob" is really Michael and switched the bodies to the freshly shot real Bob Kirkland, who would then be positively identified and buried with the CORRECT name on the grave.
When Kirkland was set to torture Jane, Jane knew he was Red John. But also he knew that if he accused him or let on that he knew, RJ would kill him on the spot. He has to convince Kirkland that he had been eliminated as a suspect in his mind. He also figured out that it was actually Michael because it was Michael's Property.
Why was RJ killing fake RJs? RJ gave him the List of 7. He's obviously trying to force Jane and the CBI to eliminate suspects until they are down to his chosen Patsy, Bertram. Jane and RJ know that accusing the head of the CBI will cause the Feds to rain hell on the CBI. That's why Jane goes with the plan and makes the big, public announcement.
How was it that Bertram was the only one to escape the blast unscathed? Because he knew it was coming. RJ set it up. When Jane took out the shotgun, he was doing what RJ wanted him to do, kill the last remaining RJ suspects like Kirkland was supposedly doing. So after Jane shoots Smith with a flesh wound, RJ or Bertram detonates the bomb, making sure all the other suspects are dead, except he loses Smith. He nearly kills Jane, which would put the CBI on a wild goose chase forever, attacking itself.