I myself haven't been in many cities during covid-19, Maz, PV, and Morelia would be it for large ones. Though I see no reason to not go to them, there have been some massive restrictions in the larger ones (Maz, PV, and Morelia were not all that strict strict when I was there, but restrictions are in place, majority of people are wearing masks). GDL for instance was closing down early, and this was supposed to be for most of Jalisco, yet the beach towns in Jalisco were all very relaxed a few weeks ago when I went through. Once you get outside the cities, especially places it sounds like you would normally go, you may not even see masks on people. I am not sure the people of San Francisco Etucuaro have even heard of covid judging by what I saw. I only say this so you keep your itinerary loose, as you may need to shift gears and get away from the cities if they tighten restrictions....but I don't think you would mind at all to be honest.