1) Gale Bertram: "Hello Patrick, I don't have to use a funny voice right? You know who this is" 
Thomas McAllister tried to use the funny voice of RJ but he wasn't on the phone with PJ because he's not RJ.

2) Thomas McAllister didn't recognize the woman in the church. How is this possible if she was another membre of Blake organization.
Because she was sent by RJ who was out of the church. She is probably Carmen Lee.

3) Thomas McAllister never said " I'm Red John". Indeed He said " I'm not Red John, Patrick, you are wrong while Patrick looking at him in the eye and He has never missed to read through the eyes.

4) Patrick is really disappoined by the identity of RJ. In fact he talked about "delusions of grandeur","ravings", "need for gratitude". PJ didn't want any answers from him, because PJ know TM is not RJ.

5) What about the discussion of Brett Pratridge and the use of verbs?
"Faking your own death was easy. Brett Partridge was Blake Association. His job gave him access to the primary DNA database. He switched your DNA records with a body that you had on ice, a surrogate, and you brought the body to my house in the trunk of your car and you put it alongside Stiles and McAllister."

If Brett Pratridge helped Thomas, why to kill him? And how he was able to choose a place full of pigeons to scare Teresa and killing Brett? If he is afraid of pidgeons in that way.