Some unanswered questions here:
When does this itinerary get you to Lima? To Cusco? When would you fly from Cusco back to Lima? From Lima back to the U.S.? What time of year would this be?
CUZ has no flights after dark. Things begin to wind down there about mid-afternoon because of weather. I'll speculate that you won't get to MP until late Thursday afternoon, which means you won't get up to the ruins until Friday morning.