I'm not sure how you bought your site admission tickets but for what you went to visit, the Cusco area ticket would have suited you and would have covered at least 5 sites that you visited. Expensive but if you manage to fit in what it does include, it isn't bad value (and not much - only half as expensive - for Peruvians).
FWIW, crowds at MP seem to thin out at or after lunch time (before the 2nd wave hits).