Let's not forget what Jane taught us, Occam's Razor. The simplest solution is usually the correct one.

If first of all we assume that the list of 7 is correct, as Heller has confirmed this in his interviews. We can move on from there. We can go through the process of elimination by matching descriptions given by the Rosalind Harker, and the latest physical description provided by Sophie Miller. 

Since we are given to understand Red John (Jay Roth) is middle aged, we can eliminate Bret Styiles.

Now, looking at Red John's build we can eliminate Reede Smith, as he his too obese to match the description.

I believe we can now safely say have successfully eliminated two of the seven suspects.

Now our next assumption is going to be to believe what Lennon told us during his die moments were true. We know that Lennon has met and seen Red John in person. But when Bob Kirkland asked Lennon “Do you recognize me?” Lennon replied no. Using this we can eliminate Bob Kirkland from a suspect as Red John.

Moving on to the more difficult suspects. Gale Bertram. This is a rather shaky and circumstantial evidence to use, but bare with me. We were told Red John has short straight hair. Whereas Bertram is bald. Using this, albeit unsatisfying, we can cross Bertram off from our list.

We have reduced our suspect list from seven to three: Brett Partridge, Ray Haffner, and Sheriff Thomas McAllistar.

On to our more dangerous conjecture, we have to believe Heller’s word, and the story up till now, and assume that Brett Partridge is dead. Please understand that this is no more believable to me as it is to you, since many of us are saying he could actually be alive since Partridge’s throat was not slit. And up till now we observed and believed that Red John murders his suspects by first slitting their throats and then carve their body afterwards.  

Now our Red John suspect has been narrowed down to just two: Ray Haffner and Thomas McAllistar.

At the moment, either of these suspects could be Red John, and we have not been given enough facts or evidence to eliminate either one. At a time like this all we have is our intuition. Let’s go back to season one. Out of all seven suspects, the only suspects introduced to the audience were McAllistar, and Partridge. Partridge has always been the number one suspect in this site up until his “death”. Leaving us only McAllistar from season one. Of course, there was that creepy encounter between Van Pelt, and McAllistar. But aside from that, let’s ask ourselves why a famous actor (Xander Berkeley) was used to portray a lowly town sheriff in the very beginning of the show. I cannot think of an answer, except for Heller’s plan to reintroduce the sheriff again in season 6. This stands out slightly to me, and makes me believe McAllistar is the “more likely” candidate for Red John.

For a summary of what we have determined here. We have confidently eliminated Bret Stiles, Reede Smith, and Bob Kirkland by carefully using the evidence provided to us by Heller, and assumed it to be correct. Afterwards we removed Gale Bertram by looking at the physical description for Red John for which he did not qualify. And then we had to eliminate our most promising suspect, Brett Partridge, because we are given to believe that he is dead. Now lastly, although we could not eliminate either Haffner or McAllistar from our list. We used reasoning to determine the more likely suspect, which is Sheriff Thomas McAllistar.

Possibilities I chose to exclude:
Although it may look like there is some kind of alliance between McAllistar, Bertram, and Smith. I do not believe it to be greatly significant as of S6 Ep 2, because the bits of conversation that was provided was too circumstantial to make any speculation. The other theory which is highly regarded is Red John is more than one person because of references to the Great Red Dragon. References from other literature are really not my forte, and I chose to leave it out of the theory.

Thanks for the read, only a more episodes to go!