I'm pretty sure that Bruno Heller had already introduced Red John in the first season (or by latest the second one), because he had no idea if the show would continue, and in the worst case, he would've wanted Red John to be atleast introduced as a person to the audience. Cross- referencing that fact with Jane's list, that only gives three names : 

1. Brett Stiles
2. Sheriff Mcallister
3. Brett Partridge

(A) Since Brett Stiles was the one who assigned Red John (the 'kid') to work in Elliston Barn (If you closely listen to Cooper on that episode), and since Partridge is the more obvious choice, that leaves only one man : Sheriff Mcallister.

(B) He was acting like a creep when he tried to escort Grace Van Pelt, so it could be obvious to guess that he could've kidnapped, raped and killed Miranda Martins.

(C) And this is the stupidest theory you could find,but Jane and Mcallister didn't become lifelong friends. You could see that the Sheriff was so pissed when he couldn't beat Jane in, after all, a normal game of Rock, Paper and Scissors...

(D) The guy who killed Rebecca had a Sheriff's uniform, and his body build resembled that of Mcallister.

(E) Simply, he's the one most people wouldn't give a second thought about, because he appeared in only one episode. The list could've contained Minelli, Masburn, or even Ron (ESPECIALLY Ron), and people would've really considered any one of them to be Red John (I did, myself, see #4298). But why, specifically, would Jane note down the Sheriff's name??