I think I got it, basically,

Timothy Carter was the "real" Red John and actualliy killed Jane's familly (pretty sure with the description of the daughter..). Thus, he was previously named "Roy Tagliaferro".

Idk what's actually linking Bret Stiles and Carter, but i'm pretty sure Brett Partridge is Stiles' son.

I noticed the famous "error" in the pilot. Partridge tried to convince the CBI and Jane that RJ killed the woman. He simply killed her himself and is the copycat of RJ. All the clues (Lorelei's, Harker's, voice...) are simply linked to Partridge who's the new Roy Tagliaferro..

In the 06x08 episode, Jane will kill Partridge thanks to the help of Smith Because Partridge is also a member of TT or Blake Association.

Lemme think what you think about that..