I buddy of mine who used to live in Silao recommended these guys. They are a chain that specializes in batteries. They have a location in Guanajuato.
Or instead of looking for a battery, just get the bike to a motorcycle shop. They will know what to do and make something work.
+1 Guanajuato is not a bad place to be stuck. IMHO the Templo San Cayetano is the most spectacular church in Mexico!
The mineral collection at the Guanajuato School of Mines is a neat attraction if you are into that kind of thing.