My theory is that Bob Kirkland is Red John.  I think that we have been seeing a combination of Michael and Bob throughout the past two seasons, and it was Michael that was murdered by Reede Smith.  The story told to Patrick about the Kirkland's childhood was true, except the brothers name's were switched.  Michael worked his way through the ranks of Homeland Security under his brother's identity, and occasionally Bob (Red John) appears as himself in order to cover his tracks without Michael's knowledge.

Bruno Heller stated that Red John is 100% on the List of Seven, and we don't know for certain that was Bob that was killed, not Michael.