Sorry that so much of the response has been negative. But it may be warranted; I don't know. My own ventures into northern Mexico have been very short, and not TM-related, but the two most extensive ones benefited from traveling with someone else who knew the area: in one case, a friend of a friend (Mexican citizen), and in another, someone I met through work (American who crossed the border frequently). I met both of these people for the first time when they picked me up at the border and stayed with them for the entire day spent in Mexico. Since you are concerned about crime and violence--and obviously, so is the State Dept, so that's not entirely misplaced--maybe you should ask around to see if people you know have a trusted friend in the area who could help. Traveling in a car with Mexican tags would certainly make you stand out less.
The adventure could be amazing and educational, but won't be if you're so concerned for your safety that you can't relax and enjoy the experience.