I am fairly certain that the indigenous ethnic group in the area of Mezquitic at the time of the conquest were Tepehuanes (Tepecanos). The Wixarrika (Huicholes) came as refugees during the Chichimeca wars and took over some of the remote villages of the Tepehuanes and absorbed some of their culture. Most of the Tepehuan communities in Northern Jalisco were assimilated into the Mestizo population soon after independence and the end of the separate legal treatment of their communities and lands. There are some communities that still survive further north in Durango.

I wonder if the location or village name provided in the left margin of baptisms might be a clue to use with historical documents or linguistic research. This was done in the missionized areas of California after mission baptisms, marriages and burials were entered into a database. A researcher (Randall Milliken) was able to map the indigenous rancherias and associate them with language families and cultural affinity, even the many tribes that had vanished. Mexico is earlier, bigger and a lot different but it wouldn't surprise me if some historians might be working on it.

well you can't from the records in most cases since the records rarely specify, and during/after the conquest many family and tribal units were torn apart/split up.