Someone hires Kira Tindsley to bug CBI. Someone chokes Kira Tindsley and purposely gives Jane the 3 dot tattoo clue. Someone blows up Jane's house and steals his gun. Someone kidnaps the 2 people without the tattoo. Someone sets up Jane for the murder of McAllister using Jane's gun. Someone chokes McAllister. No witnesses.

It can't be Red John. He wouldn't bug CBI. He already has Lisbon bugged. He wouldn't give orders to Bertram to kill Jane. There was a meeting of 3 suspects earlier on in the season; they all work for the person who really killed McAllister.

If Reede Smith shot Michael Kirkland... Bob is alive. Then Bob could bug CBI to try and find out who the suspects are. The 3 in the meeting all have the 3 dot tattoo, so Bob would give a fake clue. Bob really knows anyone on the list without the tattoo could be Red John. Bertram could be phoning Kirkland after Jane invites him to his house. Then Kirkland kidnaps the 2 without the tattoo.

I think it's likely Jane is 100% sure Partridge is Red John when we see him ignore the lady feeding pigeons, so it's possible Jane has been stringing Kirkland along, fully aware that it was not Red John who killed Kira Tindsley. I hope Jane goes to trial, and it's revealed Jane never killed anyone.