We ended up spending almost a week in the Arequipa area. In Arequipa, we stayed in Hostal Santa Catalina (500 Santa Catalina, 054 243705), which has an awesome view from its roof patio. In addition, the two men running the place are very friendly. We also found a good restaurant, Nina Yaku (211 Calle San Francisco), a few blocks north of the Plaza de Armas.
In total, we spent two days in Colca Canyon, two days on El Misti, and two days in the city to relax and wander around. We went to Colca Canyon because I wanted to spend a couple of nights sleeping at higher elevations before going to El Misti; I wasn't really expecting much from that trip and Colca Canyon lived up to my expectations. Colca Canyon isn't as impressive looking as the Grand Canyon despite being twice as deep. I'd recommend skipping Colca Canyon if you don't have any compelling reason to visit it but your mileage may vary. Monasterio de Santa Catalina in Arequipa was interesting and it's probably a better experience if you get a guide as well. We felt compelled to visit the Juanita museum after El Misti and it was a highlight of our stay in Arequipa; the textiles and mummies on display were incredibly well preserved.