So many things I want to share but I will keep it short:
1. Plan this yourself. We did; it was easy. The tour groups are terribly obnoxious. You can find good B&Bs (try: Second Home Cusco for Cusco; Second Home Peru for Lima - it is a brother / sister operation; both fathered by the living artist, Victor Delfin) and train passes to Machu Picchu. (Book train passes months in advance.)
2. When in Cusco (I second the altitude sickness meds) have the B&BS hire a car for you for the day; they can take you to some lesser known but equally as amazing ruins in the Sacred Valley. Make sure you see Pisac and Ollantaytambo.
3. Do not plan for more than a night or two in Lima. But, hit up some fine dining while you are there. Research Gaston Acurio and Israel Laura. Both are world-class Peruvian chefs. Also, Museo Larco was our favorite museum.
4. Splurge for one night on a $500 hotel in Aguas Calientes. Otherwise, do not expect electricity or a hot shower. We took the train the night before our day trip to Machu Picchu, and spent the night there (in comfort while the town lost power) before an early rise to be a few of the first people there. Also, take cash with you to Aguas - again, the one ATM may or may not work depending on the electricity situation. Oh, and do bring / wear bug repellent and long pants, no matter how hot it is. You will appreciate that you are not big bitten to death as some tourists end up.
Good luck and enjoy - you will have an amazing time!
P.S. I would do:
Day 1 & Day 2 - US Flight to Lima and to Cusco (just get there)
Day 3-4 - Cusco and surrounds
Day 5-6 - Train to Aguas Calientes / Machu Picchu
Day 7 - Cusco
Day 8-9 - Lima
Never saw Nasca Lines or Lake Titicaca but I will go back someday