I think that the key is the interview with Bruno Heller talking about the list of suspects. Actually, he didn't say "Red John is on that list" but he said "We can trust that list".

The only logical explanation for using that sentence is that Red John is Michael Kirkland.

Let's think about it a second: if those names appear in the list is for a reason and I really doubt that Jane would make a mistake on that. And the fact that Red John comes to the same list of 7 suspects make me be sure that the names are there for a logical reason. So Jane could not be wrong about the list. 

However, he had not the information that bob kirkland had a twin brother, and red john knows that PJ didn't have this information. So PJ could have shaken hands with Michael while he thought he was Bob Kirkland.

So, if Red John really was in the list, Bruno Heller would say "Red John is on the list". So Michael being RJ would explain the "we can trust that list"