Went years ago. Loved it.
Didn't do the Inca Trail, stayed at a town at the foot of Machu Pichu called Aguas Calientes. The shops literally line both sides of the railway line. Got a bus up before the hoards of tourists arrived.
Cusco is an amazing city, as is Lima too with it's colonial style buildings. Stayed just outside of Lima in Miraflores.
Also, you should go to Bolivia and see Lake Titicaca and La Paz. Take the railway line from Puno to Aguas Calientes and stop at La Raya pass which is the highest station in the world at 14,000 feet.
Word of warning, we suffered altitude sickness whilst there, drinking lots of Coca leaf tea definitely helps and doesn't get you high (unfortunately)!