There are two red johns. Lol i know. Macalister was "playing" red john for the BA. He along with partridge were faking crime scenes to look like red john did it .
Partridge was killed because he had that info.

The "real red john hasnt killed in years" as partridge said. Said not to jane, but a random forensic guy.
The murder mystery Kim was reading what about Patricks life . I bet anything on it .
Why would macalister a sheriff go to sophie miller. Give her his fear of pidgeons and then kill her by chopping off her head right before patrick found out she knows something !!!! Thats nuts !

The real red john went and saw sophie miller and gave her all lies as she thought but he really gave her the fears of the BA members !! Jane said they were clues even tho they he was "lying" to sophie .
Sophie miller is another thing to add to the "Macalister wouldn't do that list."