Stuart,
I am in the same boat you are. My husband's ancestors were from the exact same places you mentioned. The place where they were baptized, married, etc is not the same place where they were born or buried. You have to look for the phrase "originario de" for the name of the place they were born. For example, I was looking in the records of the La Encarnacion (Jalisco) church for baptisms and marriages thinking my husband's ancestors were born in the town of Encarnacion de Diaz where the church is located, then I realized that the records kept stating they were "originario de Santa Maria" which must have been a large hacienda village nearby. It seems they had big cathedrals in some towns (pueblos, villas?) where people living in the surrounding haciendas would come to be baptized, etc.
Also it seems some of these haciendas had villages in them that had chapels (capillas?), and some records of sacraments performed in the chapels ended up among the records of the larger churches. I have Mr. Platt's book, but it is very daunting. It is in Spanish, and confuses me more. I think even if it was in English, it would be confusing. So what I do is I just use whatever designation is in the Family Search Catalog for place names. It seems they kept track of the changes and they use the most current place names. A town may have had the name for example of Santa Ysabel, but now it is known by the name of some military officer, General xxxx (I forget his name). As for places of birth, I do look for the "originario de" in the record.
If it wasn't for the index (IGI) that gives me a clue as to which church's records to look in, I would be out of luck. Like you, I have no history, since my father left Mexico almost 100 years ago and never went back. He became a naturalized citizen I think when the Nationality Act of 1940 became law and all aliens had to register. He just did not want the hassle of reporting to the INS all the time.
Emilie Garcia
Port Orchard, WA ----