Patrick's father is Red John.

Lisbons brother and/or family is being held hostage and that is why Lisbon told Red John about the happy memory of Aileen or her office is possibly bugged which would indicate Bertram is involved.

Loralai is still alive or killed after making the video during the season finale. That is why the social worker went to where the baby was later at night. 

Kirkland works with Red John and had his guys steal the notes that Patrick intentionally left to see who would break into his room at the CBI. He knew only CBI or FBI could pull off breaking into his room.  That is why he left the toothpick in the door to know when to the bait had been taken.

Patrick's father / Kirkland know how Patrick thinks and was able to deduce the same list of 7 that Patrick planted. I think all 7 on the list work with Red John but Patrick's father is Red John.