To me, the list is divided in many parts:

1. People who have a major interest in finding out who RJ is- Kirkland (representing Homeland Security), Smith (representing the FBI), Haffner (representing the private area), and Bertram (who I don`t know whose interests is representing, given his weird conversation with Smith)
2. People who have a strange connection to Red John:
- Partridge is the fan (and probably one of his disciples)- he is always guessing wrongly when it comes to RJ murders, so unless he does it on purpose, I guess this could be a clue related to his death. Maybe he was working for RJ and he made a mistake. I did something wrong. I am just guessing about his death, this theory isn`t about that)
-Bret Stiles, who, to me seems to be a former mentor of Red John. He doesn`t agree with RJ`s behavior, but does nothing to stop it. I think he is feeling guilty somehow about it. 
-Sheriff McAllister - this man is very interesting and weird. Maybe he is RJ, but something tells me that he isn`t. Anyway, he definitely is somehow connected to RJ.

My point is, none of them seems to have the motive to be Red John. I`m not saying that you should agree with me, because, at this point, anything is 100% sure.  Anyway, it kinda feels like the writers are reading all these theories and introduce them into the story. The CBI Ron thing, the pigeons fear, all that seems a little too much for me. 
When Jane said to Lisbon "I could marry you off in an instant" he was actually looking very attentively at RON, like he was speaking with him. And like he was threatening him. Weird. 

Well, it;s obviously that each of the first 7 episodes aims to turn our attention towards one of the 7 suspects. The 1st - Brett Partridge, 2nd - Haffner, 3rd- Tom Mcalistair, 4th - Kirkland (see the next promo), etc. , so that in the 8th we'll find out who RJ is (I hope).
Now, it will be very interesting if Partridge will be the only dead-one of the 7 suspects, at the end of episode 7. Because that means Bruno Heller wanted from the beginning of season 6 to exclude Brett from our theories (he knows that most people suspect  him). Heller just wants that we forget about Partridge (he's dead, he's out of the list) - and so it is I see.. :)) Now, most of the last theories are about Haffner, Tom, next week will be about Kirkland, and then Stiles or Reede, bla bla.
Heller truly wants to mislead us, all the time, that's my opinion. He said in an interview that we'll be disappointed when we'll find out who is RJ. Well, actually , people wouldn't be disappointed if Brett Partridge is Red John, but the contrary.  I believe he only wants to make us thinking to a suspect which can really disappoint us (maybe Reede, or Tom or even Patrick). He is playing with us, and he tells us in his interviews only what he wants us to believe.
I still think Brett is Red John and I agree with the theories of the Revelation, 666 number and the dragon with the seven heads ... u've read about...

After watching episode 6x03 I don't think we have more reasons to suspect McAllister than we did before. What did or said doesn't prove anything. we can say he's RJ because we can see everything we know (or we are made to beleave we know) about RJ to discribe this guy!
Well no. We have not made any progress if everything he does or say can be also explained in a logical way. Why. Because then it's up to Heller to deside if he is RJ and make it happen.
Only things that could not be explained in other way than him being RJ, can be taken into account. Why? Because we have strange things for every other person in the show, that could be explained with that person being RJ.
So. What did McAllister did in this episode? CBI arrives at his jurisdiction and takes over.
The same happened in episode 1x02 and he was not happy about it, although he wasn't showing it much. Then he got emparased with Van Pelt and he didn't solve the case, Jane did.
So we expect him this time to be polite, cool, cooperative and not get in their way in a way they would get offended.
At the same time he has to show any way he can that he is sheriff for a reason and he isn't useless. And we all see that he does more than that in the end.

OK in the chapel Lisbon tells him to climb the ladder to get a hammer. Well nice is nice but he wouldn't do labor for these guys, he can get others to do work. So when he says about he would need other shoes, it's obvious that he is in the sheriff's shoes, and their errand boy. Look at the that scene. Can you see him standing like the authority he is?
Later at the cliff Jane tells him "come over here fela have a look". Well he is no "fela" he's the sheriff! Doesn't mean he's suspecious that he didn't go. And don't forget thet he was interupted.
From then on he is the nicest guy really. When Jane tells him he and his men need to hang back while Jane puts his plan to work, McAllister has no problem at all.
After he saves Jane he finaly tells him that he ignored him telling him to hang back, because he didn't trust them the way they forced their way to this case. He is still polite though. As for the pingeons flying to his face, well no one would like that.

Personaly I don't see anything suspicious about McAllister in this episode.

Just some info.

http://www.spoilertv.com/2013/10/the-mentalist-episode-604-red-listed_9712.html

This is the extended promo of episode 4.

Home Secure is watching Patrick Jane since 9 years ago. wtf? why?

http://www.youtube.com/watch?v=BxJfLgxkyWw 

So we know that Kirkland stole a fake list of RJ suspects and because RJ has the good list i think he is not a suspect anymore so we have only 5 suspects:
- Bret Stiles - Visualize church leader                                                                                           - Gale Bertram - CBI director                                                                                                       - Raymond "Ray" Haffner - private detective and Visualize member, former FBI and CBI agent        
- Reede Smith - FBI agent 
-Sheriff Thomas McAllister - Sheriff of Napa County 

From the "pigeons theory" and the 6X03 episode we know that Sheriff Thomas McAllister "He doesn't scare of high place, like the church's deck, but he hates pigeons, and he practice hunting." Probably he kill Brett Partridge so he is accomplice.

Gale Bertram - CBI director he just doesn't seem like the type. Would be surprised if he was.

Reede Smith -  FBI agent  more likely a disciple than RJ himself. But I don't think he is even that.

Bret Stiles - Visualize church leader  there has been too much that points to him not being Red John. Plus I'm sure they would want to keep him around for after RJ is gone.

-Raymond "Ray" Haffner - private detective and Visualize member, former FBI and CBI agent it's the only caracter that  have been in all the 3 "institutions"(i don't know how to call them) he was in the Visualize at the time of "Red Barn" murders.
-He and Sheriff Thomas McAllister are the suspects that appears only in episodes with the word "red" in the title.
-He shook hands onscreen with Jane.
-Probably is a former football player (like coach Amos Van Pelt, and three of Red John's friends or accomplices: Todd Johnson, Craig O'Laughlin and Manuel Montero). He has an award in his office, lightly similar at the real "Heisman Trophy" (the word "He is Man" are written by Jared Renfrew, with his own blood and before he die at Red John's hands, in Red John's Friends).Maybe He is Heisman like the trophy.
-He's shown to be a good whistler, when leaving Lisbon's room in the Hospital. Important because Sophie Miller stated that Jay Roth (Red John) is an excellent whistler.

P.S Bob kirkland it's a mistery for me because i don't think he is Red John and way he kill that man in the hospitall.I think he will die in the 6X04 episode "Red Listed"