Ah Cusco! It's been almost five years since my visit to Peru and the adventurous three day/two night trek to Macchu Picchu. It is still one of my highlights to this day.
We're sorry to hear that the first part of your trip did not go to plan and getting robbed can ruin all aspects of a holiday. We are glad things seemed to brighten up later in your trip (in a way) and that your experience at Hotel San Augustin El Dorado was more than adequate.
I am sure we will visit Peru again as Becca hasn't seen this beautiful country yet or any of South America.