If you take the actual Inca Trail it's a standard 5d trip. Trust me - you can't do it any faster!! My poor legs and lotsa ibuprofen got me through, but I still felt. If you're asking about being able to just take the train and hike around the city, then you'd have enough time in 3d, 2n. I would focus time on Cusco and the surrounding area with the day trip (go up the night before and use the full day to hike around MP).