A lot of people are asking why McAllister would deny being Red John - IMO the answer is simple, to see if Jane could tell he was lying. He looked him right in the eye and lied (and yes, Jane could tell)

I do have a bit of a love hate relationship with the whole pigeon thing. I love it in the sense that it shows us that Jane knew McAllister was RJ and that he would reveal himself in the church.  I hate pretty much everything else about it though. Lets be generous and say Lisbon planted the pigeon along with the gun so it was already there in the church, a gun strapped under a pew could go unnoticed but a pigeon? I don't think so. There is no way its going to stay quiet and still and wait patiently to be thrown in the face of a serial killer. And if the pigeon was hidden in the church with the gun, why use it at all, its only purpose (aside from telling the audience PJ knew who the real RJ was) was to distract him long enough to grab the gun. I guess its a nod to stage magicians pulling doves out of hats (or whatever) but there is no way he's concealing a live pigeon under that suit, especially not all the way from the park. I guess we have to go with willing suspension of disbelief on that one.

The other reason to hate it of course is the "Big Clue" from episode 1, the house full of pigeons was supposed to be the clue but at the same time its also the reason to discount McAllister as a suspect because he wouldn't have been in a house full of birds when he's afraid of them.

All in all, the only thing that really disappointed me about the episode was the choice of suspect. Prior to being on the "the list", he appears in 1 episode (as a red herring for the real killers too!)  for a total of like 5-10 minutes of air time. He's a total throw away character. But of the list of 7, only 2 have been there since the beginning. I would have preferred it to be partridge just because he was in more episodes. It seems unfair to the audience to make RJ be such a minor character that's never seen again until after the list is revealed. I guess Bruno Heller wanted to make it someone no-one suspected. Not a single theory on this site even considered him until after the list.

I see 2 possibilities for how RJ knew the names on the list. First, its a fairly standard mentalism trick, they show patrick demonstrating the basic principle in season 1 - when he asks Lisbon to picture a shape inside another shape and guesses correctly. Derren Brown did a similar thing in one of his shows - it was a fake ghost hunting thing and they showed how he selected the participants (basically excluding anyone who didn't pick the things they were being nudged towards, leaving him with only the most malleable people), they were given an array of photos and he talked to them while they looked at them, they were supposed to be identifying the ghost or something and most picked the same picture (I did too at home).
The other option is more mundane, its a simple matter of deduction. RJ knew what clues PJ had, they had all the same information its not a total stretch to think they'd come to the same conclusion.