Just a few thoughts - I suspected McAllister was Red John as soon as I saw the list, but I was not satisfied with the reveal. However, the fact that none of the evidence - nor was heading anywhere according to Heller - was elaborated upon means that it is entirely possible to warp the facts to fit any of the suspects, or any of the other characters.
I could create a theory that Red John was any of Jane's suspects, Mashburn. Virgil, Rigsby, Jane... and so forth, using the facts we have to support them.

As a thought for the list, is it not plausible that, as soon as Red John learned that Jane possessed the knowledge they had met, he followed the same way of thinking as Jane. We know that effectively everyone was keeping tabs on him, so it is possible McAllister could've kept himself informed of the people Jane met. Thusly, he could've eliminated people that had alibis, etc - my solution to Red John's knowledge of the list is simply that he deduced it.