I rode to Mulege a few years ago. It was a great ride and the scenery was great. The roads were in good condition. The mission church at San Ignacio is worth the side trip.The place just reeks of quintessential Mexico. And the food was good.
If it weren't for the perception of problems endemic to Mexico in general, border towns in specific I wouldn't mind joining you.
Be sure you buy the Mexican insurance.
I'm a bit leary of the border towns as well. Tecate seems to be a good crossing point from the advice of many. The more who join the ride the safer it should be right?
I'll have to look into San Ignacio!