I like beardedgeologist's suggestion. If you can, take the train to Agua Calientes the night before. The train ride is fairly long and if you take it in the morning, by the time you get to MP you've gone through a ton of transportation stress.

There is a tourist ticket, about $50 that will get you into a number of attractions in cuzco.
Cusco Cathedral
Religious Art Museum
Church of San Blas
Regional History Museum
Sacsayhuaman
Qenko
Puca Pucara
Tambo Machay
Pisac
Ollantaytambo
Chinchero
Pachacutec Monument
Performance of Andean Dances and Live music

2-3 days in cuzco, 1 day at MP, and 2 days in Lima should do it. If you end up with a full day in Lima, check out the catacombs - they are pretty cool to see, as well as the water show and one of the dinner and dancing shows.