Just got back on Saturday. Peru is an amazing country, filled with warm friendly people and rich culture and history. Next time I would love to visit Northern Peru.
We travelled there with only our Inka trail booked. It was great getting there with no timeline and being able to stay somewhere or leave on a whim. It was also great to pick our hotels as we went along, we were left with no suprises. They will show you a room before you decide. We found southern Peru very easy to navigate by ourselves. We enjoyed taking the local buses around the Sacred Valley and to Cuzco, and considered them an important part of our experience.
We enjoyed Pisac on Sunday, the market was great, although the best part is hiking above the market to the Inka ruins on the hillside. The views are amazing from up there. Also don't miss the yummy empanda place with the guinea pig castle.
We mountain biked from Moray to Salinas and then to town and found it to be a great way to explore the country side. The salt pans are amazing. We also rented mountain bikes in Chivay and again found it a great alternative way to see the town and country side at your own pace.
The island of Taquille on Lake Titicaca is beautiful, we were lucky enough to have witnessed a festival. Taquille reminds me of a Mediterranean island and it was hard to remember that its on a Lake. Also the Uros floating island were interesting and fun.
We did the trail with Pachamama Explorers and found them to be awesome. Some Inka trail alternatives: We met several groups of people that did the Salkantay trek and loved it. . Also, the hike to Choquequirao seems wonderful also, they are still excavating it, and it is believed to be larger than Machu Picchu, although not of the same importance.
Fellow vegetarians- don't worry to much. I found no problems finding plenty of great food. Most place offer vegetarian options and even have vegetarian versions of traditional plates. Vegans, may have a bit more trouble.