How about this: Haffner is Red John, and he is also Michael Kirkland.

-He altered his appearance at some point, which explains Kirkland's killing people who don't recognize him, which means they obviously didn't work directly with RJ and were of no use to Kirkland.
- He is not a member of the BA, just knew about them and used that knowledge to his own advantage.
- How could a bomb have been smuggled into Jane's house?  It's not in a hat or a coat. It must have been done in advance by RJ, who knew the place Jane would most likely stage the "unveiling." He had been there before, when he killed Jane's family.
- Since the two remaining living suspects don't really match up to what we know about RJ, then one of the "dead" suspects must have faked his death. The best way to do it? By bringing Kirkland's bomb-laden body to the house ahead of time. That kills everybody involved, makes it LOOK like Haffner is dead because his DNA matches Kirklands, and allows for Haffner to disappear and start over.
- Now the world believes Bertram is RJ. Haffner/RJ goes to the church to gloat, or whatever the hell a psychopath does in that situation, and gets shot, flees, but is caught and strangled by Jane.