No, I'm not sure of the origins of Rubalcava, although I would not be surprised to hear that it is a Basque name. Obviously there was a very strong migration of Spaniards and other Europeans to that central/Bajio part of Mexico (as well as other parts). As far as settlement patterns go, I have not confirmed this but my hunch (based on prelim research) is that the earliest settlers of the region came up from Mexico City, through what is now Jalisco and set up the first outpost in a place called Nochistlan (Zacatecas). They named the settlement Guadalajara, but had to retreat/abandon it due to conflicts with the indigenous people. So the settlement of Guadalajara was moved south to its present location in Jalisco. Nochistlan still exists however (they didn't completely abandon it) and I believe it may be a good source of local data pre-1700. It is in Zacatecas, just across the border from Calvillo.
Calvillo's records are good, but not great. I think the LDS Church has done a fair job of indexing it, although there are holes in the archives. I think they date back only to the 1750s, but i'm not certain.
Do you have any sense of the immigration records into Mexico? I haven't gone that far back in my own family history (i'm still working circa 1780), but i wonder how the Spanish provincial government tracked immigration flows into Mexico. Are there records for cargo ships, etc? Did the ships arrive at one port in particular? Was there a documentation process for immigrants? Any thoughts on this would be helpful.