Maybe the clues are in the paintings by William Blake. The great red dragon and the beast. The number of the beast is 666 again written on the wall of the house Lisbon was in. William blake seems to be a reoccurring theme along with the pigeons. The upcoming episodes is called the great dragon. Blake once claimed that he got the idea for the illustration method from a vision of his dead brother( not sure this means anything but interesting anyway).
This is what it says about the beast: ".....................and the (great) dragon gave him his power and his seat, and great authority". Could this have to do with Stiles giving Red John Power? I do hope we learn what these clues all mean by the time RJ is caught.
Also what did the wall say in that same house was it DIE or PIP or DID? I couldn't see it properly. The clue had to be in that room she first into because there was nothing in there and it was a waste of footage going in there in the first place.