I think Partridge really is dead.  The reason he is dead is that he was RJ's forensic guy!  He examined every crime scene to remove any evidence that would lead back to Red John.  That's why we see him at every RJ murder scene, and that's why he was the first to be killed.  He knows all the evidence that would link Red John to his murders.  He knew waaaaayyyy too much.  Thus, he was the first to go.

Ultimately this will be RJ's undoing.  Partridge was kind of the brains of the operation.  He kept Red John two steps ahead of everyone.  Now that he's gone, RJ has started being careless and making mistakes, letting Kira Tinsely see his tattoo, not destroying Sophie Miller's voice recorded sessions.  Partridge would have totally figured that out and destroyed the tape.

Regardless of who you think RJ is, Partridge is the forensics guy.  It explains quite a lot.  I still say the Sheriff because he has indicated he's been a hunter most of his life and enjoys killing.  He's an intelligent man, but not the brains of the outfit, so without Partridge, he really shot himself in the foot!

The only person out of the 3 with the tattoo who could have killed the private detective woman is McAllister.

Bertram is 6'3, Smith is 6'2. 

When the woman opens the door, she doesn't look up. Their eyes are on the same level.
She is not a giant like those 2 men, in fact she is about Cho's height.

The only person who is not above 6 feet is the sheriff.

I don't know if he is Red John or not, but out of the three it can only be him who killed the woman.

So I have a theory on the 7 suspects on Jane's list.  Why does he choose these 7 people?  What's so special about them?  I believe some are on the list because they are suspects, while others are merely accomplices.

Brett Stiles.  Jane thinks he's an accomplice.  He's never shaken hands with Jane, but Brett has always hinted that he knows RJ's identity.  We know there's a connection to visualize.  Jane puts him on the list because he believes Stiles will either willingly or unwillingly help him reveal RJ.

Gale Bertram.  He's an accomplice.  Jane knows he doesn't fit Rosalind's description of under six feet with short straight hair, but the man is in on it.  He's the director of the CBI and basically owns the Red John case.  He's always telling Jane "I wanna be there when you reveal Red John".

Ray Haffner.  He was a suspect, and a damn good one.  But he ain't RJ.  I don't believe he's actually involved.

Reede Smith.  He's an accomplice.  Jane never shakes hands with him, but RJ states in season 4, "...luckily I have a friend in the FBI".  Jane has deduced  that Reede is his FBI accomplice.

Bob Kirkland.  He was a suspect, but Jane discovers he was merely hunting RJ... oh and he's dead now.

Brett Partridge.  He ain't RJ, cuz he's dead, but he's very important!  What does he do for a living? Forensics!  Where do we always see him?  RJ crime scenes.  He's the guy who cleans up after RJ.  He makes sure no evidence can lead to him.  This is why Red John kills him.  Partridge knows vital clues and information that in Jane's hands, could identify RJ.

Sheriff Mcallister.  He's a sheriff in wine country.  Not much to contribute as an accomplice.  Not much jurisdictional prowess.  Therefore he has to be a suspect.  As I mentioned previously, they do not physically shake hands, but Jane and Tom play rock paper scissors, where-in you shake your hand repeatedly before revealing either rock, paper or scissors.  Therefore, they "shook" hands.  He's a hunter and as he tells Patrick, he knows how to "clean and quarter a kill".

Incidentally, what do hunters always do to their prey after they shoot it?  They cut the throat and let it bleed out.  What does RJ do to all his victims?  He cuts their throat and watches the life leave their eyes.  Plus, the knife RJ uses is quite possibly a hunting knife.  Take a look at this scene where he saves Patrick.  First he shoots a victim, then he slits her throat.  Plus the knife certainly looks like a hunting knife for quartering and cleaning a kill.

http://www.youtube.com/watch?v=MKZvmwU1ufg

Just watch my video, its 4:29 minute long. Dont forget to pause if you don't have time to read and a like would really help! Hope you enjoy! :D

  http://www.youtube.com/watch?v=ohIxFnOnRCk

So Americ from Happy Cool posted a very good theory about Red John entitled "The Handshake Theory".  In this theory, he points out the handshake had to have been onscreen.  Otherwise, why even bring it up?  I believe this is true.  Sure he could shaken hands with some of the suspects off screen, but would that really be very good story telling?  I don't think so.

So Americ goes through the list systematically to see who Jane shook hands with onscreen.

Brett Stiles- did not shake hands
Brett Partridge-did not shake hands
Reede Smith- did not shake hands
Ray Haffner- they shook hands
Gale Bertram- they shook hands
Bob Kirkland- they shook hands
Sheriff Mcallister- they did not shake hands

So Bob is dead, and Gale doesn't fit the physical description.  Thus leaving Ray Haffner.

BUT

Here's the rub.  We HAVE seen Jane and the Sheriff shake hands... just not in the traditional sense.
They're very first scene together, they play a long game of rock, paper, scissors and Jane keeps winning over and over again...  What do you do every time you play this game?  You shake your hand three times before revealing either rock, paper or scissors.   Thus, Sheriff and Jane "shook hands" the first time they met, just not with each others' hand.  :)  It's a very iconic scene from the first season.  Take a look at the first part of this video to watch it!

http://www.youtube.com/watch?v=0w_Oc5wOeWw

Guys it physically can't be Bertram!  How are people still on this?  He is 6ft 3 and bald which flies in the face of Rosalind's description.  "Under six feet.  Short, straight hair."  Jane COMPLETELY believes that Rosalind's Roy is Red John.  He even took her to the morgue in season 4 to confirm the man he shot in the cafe WASN'T Red John.  Ere go, he trusts her account of Roy as if it were gospel.  Could Bertram wear a wig?  Perhaps but unlikely.  However what is far more unlikely is that he can't cut 4 inches off of his height when he's with Rosalind.  Plus Bertram is a public official who spends waaaayyy too much time in front of the camera.  He would have been easily noticed by Sophie Miller who would in turn probably ask what Jane's boss is doing here.  She would've known right away something was up.  Plus the director of the CBI probably has zero time to go around killing people.  That kind of job requires far too much time at the office and in front of the camera.  A Sheriff of one county is a well-respected official with many friends and quite a bit more freedom to go where he pleases.

Sheriff Mcallister is both marked and a marshall (the whole he is mar thing), fits the height, fits the build "not thin, but not muscular", he loves to hunt/kill as he informed to Jane.  Tom asks Patrick to call him "Tom" because he wants to build a relationship with Patrick, wants to befriend him, as we've seen Red John do with sending him Lorelei  "He's offering the hand of friendship".  In regards to his hair, he had much more 6 years ago when he was cast so Rosalind would have called it "short and straight".

On a side note, some people mention that we never see them physically shake hands... but we do.  In they're very first scene together, they play rock paper scissors, within which you "shake" hands multiple times... :)

Jane: What do you hung?
Tom:  Anything with a face... 

It's not him because Bred Styles knows who RJ is. That I'm sure of.
And in Fire and Brimstone Bred Styles 'saves' him from beeing shot by Jane,
because he knows he isn't Red John and doesn't want an innocent one beeing shot.
If he was RJ I think Styles wouldn't try to stop Jane.