Alright, I've worked on a theory for a bit, and would love to get feedback. Again, I'm sorry if any of this has come up before, I really tried to catch up but I had to finally call it quits because if I see one more bird of prey I suspect that my eyeballs will shrivel up and fall out...
One of the names on our list of potential matches is Thomas Michaud of Colorado.
https://www.findthemissing.org/en/cases/21237/55
I don't remember who, but someone here suggested that they believe that John Doe was killed by a relative. Now, I haven't been able to find much backstory on this person, but there is a notorious serial killer and rapist couple by the names of Michelle MICHAUD and James Daveggio who were active in the Reno/Tahoe area as well as the Bay Area. The two of them are absolutely evil. Here is some information about their crimes, but it's really disturbing so be careful...
http://www.sfgate.com/news/article/Sex-torture-killer-Daveggio-given-death-penalty-2767057.php
http://murderpedia.org/female.M/m/michaud-michelle.htm
Their MO also jives well with some of the other theories I have seen here in the thread.
John Doe may have been a crystal meth user on account of the condition of his teeth. Daveggio and Michaud also used meth together during their sick "adventures" as she called them.
I'm unsure where Michelle Michaud was born, but I did find a Thomas Arthur Michaud born 8/9/1952 in San Mateo county, CA in the CA birth index. May or may not be the same TAM. The missing person profile at
https://www.colorado.gov/apps/coldcase/casedetail.html?id=112
lists his DOB as 8/10/1955. Interesting.
M Michaud and Daveggio's crimes were also of an extremely sadistic sexual nature. It was suggested a while back that this man may have been killed during a sexual interaction because only a shirt was found.