So I would like to propose an idea entitled The Severed Foot Theory

As Lisbon enters Jane's demolished house, she waves her flashlight around and comes upon a severed foot.  I postulate the foot was NOT blown off by the explosion, but rather a shotgun blast... the same shotgun blast we hear prior to the bomb.  

Here's what happened.  One of the suspects grabs the shotgun out of Jane's hands.  He's aiming it at Jane, who panics saying, "No! WAIT!"

And then the strangest thing happens.  The suspect shoots off his own foot!  Jane is perplexed for a moment, and then the bomb explodes.  Due to head trauma, he forgets that last split second.

So why was the foot blown off?  Because the suspect wanted the forensics team to find it.  That way they would believe him to be dead.  This would also imply the suspect knew about the bomb, and therefore would probably be Red John!  

My theory eliminates Bertram and Smith because they have both of their feet.  So it has to be one of the supposed dead suspects: McAllister, Haffner or Stiles. 

From what Reede Smith tells us, someone within the Blake Association wanted Bosco's secretary dead.  Therefore, I put my money on McAllister, since he's got the tattoo.