I know there are some areas around San Miguel where you can ride on trails. I've been to the city Guanajuato which is very similar to San Miguel and not too far away from it. The only cobble streets there were in the center of town and the same might be true in San Miguel.
You mentioned there is a decent bike shop in town. I would suggest giving them a call and find out some info from them. If you don't speak Spanish, I am sure you'll be able to talk to someone in English. San Miguel is a very touristy town with lots of Americans and I would assume people in business there would be familiar with English.
Good luck and I know you'll have a great time.