Points to ponder
Perhaps I'm mistaken, but it appears that when you see Jane (plastic)tied in the chair, the ties are around his coat sleeves. But when the torture threat is made, and the weapon is moved to (his) thumb, there is no coat. And the shirt sleeves that are rolled up are not of the same shirt worn with the coat.....
I vaguely remember that Jane has said that Red John makes mistakes. Was it not Bosco who first told Jane that when he was on his death bed? And did he not whisper something to Jane that we didn't hear? I know he told Lisbon that Bosco wanted him to protect her, but I'm thinking he might have told Jane what mistake Red John makes, and to be ready to recognize that later on.