My suggestion is to stay in Cusco for the week. Take it easy the first day there just to acclimatize. Maybe hike up to Sacsayhuaman in the afternoon. Next day, you can go further out and visit Quenko, Pukapukara, Tambomachay. After that there is Pikillaqta and Tipon a little further out.
contemporary sights around Cusco, Santo Domingo or the Art Museum in the old Garsilaso house near Plaza de Armas.