I surely do think Red John is dead and done with.

That said, I'm not so sure about Stiles...  Yes, he said he was dying, but perhaps he was getting out of the line of fire so to speak?  If he knew Jane was getting close, and if there was some sort of relationship between Stiles and Red, maybe his dying 'story' would allow him to disappear if Jane found out and defeated Red John...  Maybe Stiles got blowed-up good anyways despite a relationship... 

Tom might have had the DNA records switched with two bodies to save Stiles as well...

Stiles might just be talking the talk when he says he knows more than Pat or John could ever know, but then again, he might be involved--the whole Tyger group... 

I don't know how, but I have a feeling we aren't done with Stiles.  The girl who tried to knife Jane at the end of 'Red John' sounded like she was from Visualize to me.  We also know that Stiles is very manipulative and followed.  That and he definitely has the resources which could have helped a NAPA County sheriff do what he did...  But so did many other members of Tyger I'm sure...

When the FBI rolls in at the end during 'Red John' we see an old man in a suit walking away with white hair...  Waldo?  Stiles?

I think bringing him back would be a smart idea from a writer's perspective--he'd make a good finale.  Stiles would allow the Mentalist to end this season (and possibly series) with some familiarity, yet something new as well.  A link with Visualize could help answer some burning questions we have left over.

So while I think John is gone, Stiles might show himself again...  Perhaps he along with Michael Kirkland...  I don't think that Tom necessarily followed Stiles, but some sort of relationship could clear-up some of our questions...  

But of course, maybe Stiles was just talking the talk.