This is not really a good theory about who is Red John, It's more about the relationship between Kirkland, Bertram, Reede Smith, McAllister and Darcy.
I think that they all think Jane is Red John (for some good reason, I hope), remember, Darcy says something about it in 4 season.
Kirkland is watching Jane since he became a CBI consultant. So, Kirkland called this "time" to keep an eye on Patrick.

But we all know that Jane is not Red John.

I think Red John is Thomas McAllister. He is taken out from suspects by not having fear of heights at the end of the episode, but he is afraid of pigeons. In S06E02 we learned some things about Red John, including that he may have a fear of heights and can whistles really good, all those things have been explored, but not the pigeons. They appear in the first episode of this season and has not yet been cited by Jane or anyone besides. Still in S06E02  the camera focuses in the hands of this strange lady who is feeding the birds. 
I believe that Sheriff Thomas McAllister is cheating with Kirkland and all others. 

I also believe that there is an important role for Bret Stiles, there must be a reason why he has been included in the list of suspects: Shortly before the list episode , we learned that Red John is a middle-aged man, who had less than 30 in 1988, in addition, Stiles does not match the Rosalind description.

I am Brazilian, and I don't speak english, so i don't know if I made myself clear. If you can't understand something, please comment and i try to write better. And I'm sorry if someone posted some theory like mine before, i never see one similar.