The clue is so far that jane and red john shook hands and they've met but didn't become best friends ! the writers put the pilot episode in season 5 of the series and if you look again you'll see in that story jane shook hands with the JUDGE and when lisbon and jane investigate him he says if you want to hurt a man don't kill him kill his family !! and right after that he asks jane if he has children!!
this maybe be a possibility!!!
p.s Kirkland is for sure an accomplice and Alexa is that friend of red john's in the FBI.