1, The dark version: Jane is the schizophrenic mastermind behind the Red John mask. His family's death, that could've been the real Red John, but during mental breakdown and rehab, Jane lost this marbles and guilt made him become Red John in a split personality kind of way. While hypnotizing his victims, he agrees on a secret pact a la Fight Club "we never talk about that it's me, and even when we meet inside the police office, and I question you, you will have to pretend that we don't know each other and keep our little secret". During daytime, Jane has to catch up on some z's from his night activity, that has no clue about (Also a Fight Club theme). John and Jane. Two sides of the same personality. That time when Red John appeared behind him, being tied to a chair in the abandoned hotel, that was all in his mind.
2, The semi dark version: The one time in the mental institution, that wasn't his only time wearing a white skirt. Jane is an unstable fellow, in and out of institutions since his wandering circus childhood where he accidentally killed his little twin brother John. Since then he has had "visions" (Kristina was right , he has the gift). But for him it's a curse, because John keeps reappearing, blaming him, possessing people and making them kill, giving Jane work to do. At night Jane sleepwalks into fresh crime scenes and unearths clues to his brother's killings for the daytime Jane to stumble on during next morning's police investigation. That time when Red John appeared behind him, being tied to a chair in the abandoned hotel, that was actually the ghost of his dead brother that the eventually healed Kristina will one day see and persuade to leave peacefully. Whoa, happy end.
3, The little bit dark version: Jane is Red John's mole. During mental rehab after his family's death, Red John hypnotized Jane to act on his will by a secret word that turns Jane into the murderer's zombie assistant. Jane has been unknowingly supplying Red John with case material ever since, putting Red John one step ahead of police each time. Jane is also present when victims get hypnotized, that's why they recognize him as the accomplice "who should know". The constant sofa sleeping, that is again Jane resting from his assistant night job. That time when Red John appeared behind him, being tied to a chair in the abandoned hotel, that was his master he didn't recognize, because the code word wasn't spoken. But through sheer will power, Jane will first uncover, then overcome the mental manipulation, Red John gets arrested and the show goes into a new season with a new villain. Hooray.
I personally prefer 3, but all in all, whatever the final explanation will be, it must answer why Jane sleeps so much and why victims laugh at him in surprise when he asks them who Red John is. Am excited to see what other possibilities lie in the answers to those questions, that the wonderful writers of the show will roll out for us over the hopefully many seasons to come.