There's lots to see and do in Cusco and the main site at Urubamba (Ollantaytambo?) is especially impressive. Besides touring the Incan ruins, there are other fun activities such as horseback riding and white water rafting. Having said that, if I were putting the trip together, I'd probably add a day on the Amazon. I took a very similar trip last summer and the Amazon was an amazing experience.
I recommend that on Day 3, you spend the night in Aguas Calientes. Macchu Pichu often looks completely different first thing in the morning. Being on that first bus is totally worth the effort.
I want to reiterate SJOGuy's suggestion regarding the order of the trip. It would make more sense to place Puerto Maldonado immediately before or after Cusco.
One final recommendation - If you can get a reservation, I highly recommend dining at Astrid y Gastón in Lima. It's ranked as one of the 50 best restaurants in the world. Try the Peking cuy!