I found this very interesting http://www.whoisredjohn.com/See-a-theory-Red-John/6392 7 heads = 7 suspects in the list.
So, my final theory is that RJ REALLY WAS Bradley Whitford. Then the CBI people decided that they needed to bring PJ back to help them solve cases, so they all worked together in order to make him believe that RJ is still alive. Hence the meeting in Bertram's office and the line "how much does Jane know?". This would also explain what happened to Lisbon and the 7 heads.
