Did anyone else notice the teacup?  In a season finale a couple years ago, when a redjohn accomplice had Jane in the basement of a house, Lisbon rescued him before Jane was ready.  They showed the upstairs where there was a half used teacup sitting on the kitchen table and the patio door closing.  I think it was the same teacup that Jane was drining out of last night that the FBI guy knocked it out of his hands.  Jane said "hey, that's my favorite teacup."

My thinking is that Jane knows from the teacup who RJ is.  He now has DNA for the 5 "dead" people to run the DNA from the teacup against.

At this point, there are very few things I'm very positive about.  1 is that Reede Smith is NOT RJ.  Jane interviewed him and dismissed him and as Bruno Heller put it, if Jane says it's true, you can take it for face value.  2 RJ is the leader of Tiger, Tiger.  It's his organization to cover his tracks using dirty cops who are afraid of being discovered.  3.  The FBI was sent in to close down the CBI as a Tiger, Tiger order. 4.  There's more to Partridge's tattoo being cut off than his tattoo being cut off.  There was too much emphasis on it, and Jane deflected Lisbon's question, which tells me to pause there.  5.  Jane taking the gun from his house hasn't played yet.  6.  Jane knows who RJ is at this point and is going to the church to let things play themselves out. 

Beyond that McCallister is a guess.  There are at least 3 plot twists coming in the next episode and the first reveal is DEFINETLY NOT going to be RJ unless there is an end-story followed by back story.