After re-watching RED HAIR (2nd episode of Season 1) and CRIMSON HAT (last episode of Season 4), I feel that Red John can definitely be Thomas McAllister.

In RED HAIR ... while Lisbon and Jane are interrogating the drug dealer/boyfriend of the murder victim, the Sheriff is in the room too.  Before the boyfriend answers Lisbon, he looks at the Sheriff - who gives him a signal by squinting and cocking his head.  At this point, the boyfriend tells his story.  He looks at the Sheriff again later in the conversation after being asked another pointed question from Lisbon.  Keeping in mind that Red John has many types of people working for him, the boyfriend could be an associate.

The husband/wife (owners of the restaurant) who turned out to be killers, could also have been working with Red John/McAllister.  He may have been at the restaurant the night of the murder to provide cover for his associates, not answering a call about an unruly customer as he said he was. 

There was also the obvious scene where it looked like the Sheriff was attempting to kidnap Van Pelt.  Perhaps he knew about the CBI plan (through one of his contacts) and was attempting to distract them while the husband/wife kidnapped the other red head at the restaurant whom they brought to the hotel room to kill.  They were killed, so there's no way to know if they were Red John associates.

Finally, at the end of the CRIMSON HAT episode - after the FBI has shot at the limousine and mistakenly killed the head of the CBI - a police cruiser drives by.  This has been mentioned in other theories.  When you slow down the scene, the driver can very easily have been Sheriff McAllister.  Perhaps he was there to speak with Jane in the limousine (via the phone), of perhaps he wanted to observe what happened.  In either event, the police cruiser sped away...but for what reason??  The shooting was already done and the FBI/CBI were taking Lorelei, not the police.

McAllister could be Red John.