So here's a thought...what if Red John is Michael Kirkland, Bob Kirkland's twin brother?
Bob hesitated when Patrick asked him if Red John killed his brother and answered in a way that seemed very much 'he killed the brother I knew, he's as good as dead, etc.". His body was never found and he was never heard from.
The Kirkland brothers had a rough and abusive childhood, which clearly manifested in some psychosis on the part of Bob and caused his brother to spiral downward.
Patrick could have shaken his hand at any point thinking he was speaking to Bob - it would be easy for Michael to accomplish this as a twin and with the manipulating skills we know Red John to possess.
Also, this would add some wow factor the the big reveal, as he is not on the list of suspects that we have left, but only because Patrick may not be aware that he encountered the twin, rather than Bob.
Thoughts?