I think it might be possible that this entire time, Jan has been Red John but doesn't know it. After the trauma of his family being killed (by a killer for a different reason), he developed a multiple personality disorder and created Red John to make sense of it all. In a way it is like the movie fight club. Jane is the master mind behind all of "Red John's" doings and the people who follow Red John. The only reason this may work is to think that Jan has no idea he is also Red John. He can not be in two places at once, but I have no doubt, if he is Red John; he's had people do some of the work for him so he could be Jan while "Red John', is still at work. In one aspect I would hate to see Jane be the bad guy, I love the whole team, but it would make a crazy ending to the series.