Red John, has something that the US government fears. Just like Moriarty having the "key code" in Sherlock. He has progressed from a serial killer into a full-fledged consulting criminal. The government has to play by his rules, which probably includes killing his followers if every they get caught, and prevent Jane from getting closer to him. So basically he is pulling all the strings. Red John is a sociopath who is easily gets bored, and Jane seems to be a perfect distraction.
Robert Kirkland is NOT Red John, or his follower. He seems to tracking Red John for many years, but can't get a hold of him.
Red John is definitely part of a humongous machine.
"That is not danger," said he [Moriarty]. "It is inevitable destruction.  You stand in the way not merely of an individual, but of a mighty organisation, the full extent of which you, with all your cleverness, have been unable to realise.  You must stand clear, Mr. Holmes, or be trodden underfoot."
And Patrick Jane will soon know what he is up against.