It's not Partridge, since he is dead.
I think the phone tracking maps might be the clue in the final scenes. Since there were no other phones showing up co-located with Partridge's, we can assume RJ left his phone somewhere when he went to kill Partridge. Which is also why he used Lisbon's phone to call Jane. That makes sense, as he knew about the tracking. So, if his phone was left somewhere, it likely isn't "in transit." According to the map Lisbon was looking at, that should eliminate Stiles, McAllister, and Haffner, who were all in transit during the murder. So that leaves Kirkland, Smith, and Bertram. Smith and Bertram don't fit the physical profile of RJ, which we know from the few times he has been seen, and also from the description by his blind girlfriend. That leaves Kirkland, who left his phone in LA when he realized he was being tracked, and went to Sac. to kill Partridge.

I think he killed Partridge because Bertram thinks Kirkland is on the up and up, and is working to find Red John. Bertram must suspect Haffner, who was inside the CBI. Which explains why he and Kirkland discussed whether they can trust Lisbon. Would she blab something to Haffner, accidentally or on purpose, that would compromise what Bertram thought he and Kirkland were doing? Partridge's death will validate Haffner's guilt to Bertram.

But who really knows? RJ could have purposely left his phone in a taxi, so that it would appear to be "not left behind." And there are still a lot of things that don't make sense. Where WAS RJ hiding when he popped out and grabbed Lisbon? That suggests it had to be Partridge, "hiding in plain sight." And is it true Jane didn't meet Kirkland until AFTER he was told about the hand shake clue? That suggests it ISN'T Kirkland. I hope it all makes sense after all is said and done.