Head hot the hills as soon as you hit Lima. Get ready for a death defying flight to Cuzco.
I had a ball in Cuzco. The only negative point I could bring up is the children in the streets trying to polish your shoes(or thongs, flip flops in some cases). Or trying to sell finger puppets, very persistant little buggers.
My friend Chris and I had no trouble booking a tour group for the Inca trail/trek from here.
The Inca trek was fairly tough in places. The major problem being the altitude(or lack of fitness on my part). We did the trail in late may and the weather was perfect. Warm enough to get a tan and cool enough to look at beautiful snow capped peaks all around you. Definately do the walk, don't be soft and take the train to Machu Picchu.
When you get to Machu Picchu, take the time to climb Hyuna Picchu(sorry if spelling is incorrect!) Its the mountain that is typically shown in all the photos of Machu Picchu. It takes about 1.5 hours all up and is supreme in its ability to satisfy those longing for the best view in the world, or those with energy to burn. Its not as difficult as it looks, I shared a path with a group of Japanese folk at least into the 70's!!.