Heller said:"There is a clue buried in that final sequence that will pay off big time
in the finale of the Red John story. A very big clue. No one will get
it from the clue as it is laid out in the episode, but it will pay off
later."

Sophie Miller says that jay roth has a phobia maybe achrophobia (fear of heights)
she's not sure about it.

then I thought of what patrick told lisbon in the hospital about why rj didn't kill her.He said:" Maybe something spooked him and he couldn't go through his usual routine"
Remember what was in that house in first episode?PIGEONS
Lisbon left the door open so pigeons could get out of the room.
that is the big clue heller told us about IMO.RJ fears pigeons
in fact at the min.28:59 we see someone feeding pigeons and patrick staring at them