We found Hospedaje Casa de Manzanos online and decided to stay there after calling about 5 different places. It cost us $100 for three nights, including a tip and breakfast one morning. Plus mangoes and bananas. It included a small kitchen with a sink, stove, fridge, and microwave. There was wifi and plenty of hot water, and bottled water was supplied too. I thought it was a great place.
I also liked its location because it was on a callejon but we didn't have to drive through Guanajuato to get to it. It was easy to find and we parked in a public free lot at the bottom of the callejon all three nights with no problem. It was about a 20 minute walk into the historic center and there were plenty of buses that cost about 50 cents for a ride.
As you'd expect in Mexico, we ate well for $10 per day for each of us.
I'll post about the places we saw later. We were able to see pretty much all the sites in Guanajuato in one very long day. Two shorter days would have been better.
I kept reading that we shouldn't drive through town, and people in Mexico told us that, but after walking all over on foot on Saturday, we thought it didn't look too bad and tried it on Sunday and Monday with no problem. It was fun to drive through the tunnels and much quicker to drive through than go any other way. I wouldn't have wanted to drive into town without knowing anything about it and try to find a certain hotel in the dark, but I wouldn't hesitate to drive there again.