Like I said before I have always found the two day Inca Trail very expensive for what is basically one day of hiking. If you don't do the Inca trail you have 4 days for Cusco, the Sacred Valley and MP. You could go to the Pisac ruins on day 1 and then continue to Ollantaytambo (don't miss the ruins). You have two options for MP. Take an evening train on day 1 from Ollantaytambo to Aguas Calientes, day 2 visit MP and take an evening train back to Ollantaytambo. Or take an early morning train to AC on day 2, visit MP and take an evening train back to Ollantaytambo (no overnight in AC). So the morning of day 3 you can go back to Cusco and visit Moray, the Maras salineras and Chinchero on the way. Day 4 would be for Cusco and the ruins north of Cusco (don't miss Sacsayhuaman).
I would consider skipping Arequipa. Yes, one day for Arequipa is enough and the Colca valley tour can be done the next day (although that would be a very long day as I pointed out in my last post). But if you skip Arequipa you would have two extra days for your trip from Paracas to Cusco.
Or you could skip Paracas because you might find Arequipa and the Colca valley more interesting as you are more into people and cultures and less into landscape.
If you do take the train to Aguas Calientes you should buy tickets online (Peru Rail or Inca Rail). You can buy tickets for MP here:
http://www.machupicchu.gob.pe/
Tickets for 2017 go on sale late December. You can choose to climb one of the mountains at MP. We climbed MP Montana and loved it. The other one is Huayna Picchu.