We've traveled through Mexico many times. Our plan of action was always to get out of the border areas ASAP. To facilitate that you stay overnight in the US and cross into Mexico first thing and get as far south as you can and want to. We usually shot for a good 4-5 hours south of the border. Coming north we would stay 4-5 hours south of the border, get an early start the next day so we'd be stateside by sundown.
Typically the gangs are not out to do anything to tourists so you should be reasonably safe.
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