In reply to Blue Straggler:
I did the Machu Picchu trek with my sister sometime around the turn of the millennium, so not the most up to date.
We just arranged the trek after arriving in Cusco.
There was one col of over 4000m that I remember where she paid a wee lad to carry her rucksack for her. The trek leader was very knowledgeable and the arrival at the ruins was timed for early morning to make the most of the day. At the time you could walk up Huayna Picchu at will. I did this and would definitely recommend it.
I spent the next couple of weeks exploring the country on my own. I went to Huaraz and did a solo trek and a guided trip to Chavin de Huantar, both memorable.
I then headed north to Trujillo and visited a number of archaeological sites, along with Huanchaco for a look at the reed boats and a plate of ceviche. Not many tourists around.
Other than Lima (great museums), the other place I went to was Arequipa, a great town with a super climate. I went to see the petroglyphs of Toro Muerto (ace!). It can be a base for the Colca Canyon and I had a trip booked but unfortunately I couldn't make it (be careful who you trust!).
I travelled by long distance bus and really enjoyed the experience. You could choose your seat, there was a video, toilet, lunch provided and a game of bingo.
If I were able to go again I'd look to go further north to Cachapoyas, inland to the rain forest and some of the desert stuff down south like Nazca.
Do it, but organise things yourself once you are there. Cheaper and more flexible.
Jase