I'll preface this by saying I DON'T actually believe this will turn out to be the csae, but let me propose a scenario.
RJ killed Jane's family as outlines in the story, what happened then? What if at some point Jane discovered the identity of RJ and managed to exact his revenge. Now, without a family or a cause, he has regressed psychologically to a point before dealing with RJ. Everything since that point has been Jane's doing. He has been behind the larger "conspiracy" and the assistance of several acolytes allows for the presence of holes in logic presented by Jane's being the culprit.
Again, I don't think this will wind up being the case but it is technically feasible and would be an interesting twist while still allowing for Jane to play both the role of RJ as well as the damaged victim not entirely in control of his actions due to those of the "original" Red John.
Just a thought