We have been to both Peru and Brazil. I add Brazil as this was the Amazon trip into an Eco Village. Peru was specific to see Manchu Picchu. Both trips were booked through adventure companies.
Peru we stayed in Lima for 3 days, flew into Cusco (2 days) and then spent 3 days in the sacred valley before going on to Manchu Picchu (1 day) and returning to Lima (3 days) . As we are older and my wife does not walk all that well we decided against the hike so we did the train. Highlights were the Museums in Lima and Cusco, walking around Lima, the sacred valley - people and ruins, Manchu Picchu and the mountain across (Winna-Picchu (sp)). Watch out on hygiene and take lot's of handy wipes for washrooms (sink handles), cutlery etc. Misses were not staying an extra week and going south to the other ruins (Mud Pyramids). Manchu Picchu can get busy -- when we were there they said there were 5K people on the site and it was not considered to be a busy day.
Brazil - Eco Village -- no power, in the heart of the jungle, unbelievable insects, amphibians, noise, heat and humidity --- would go again in a heart beat.
I would start checking with adventure companies as they can get micro tours of 3 to 5 days that are off the beaten path. ie if you go to Iguazú Falls do you want to stay in 5 star accommodation or a tree top cabin? -- do you want to go to -- Lake Titicaca or the Mud Pyramids. There is more to tour than a person can see in a month.
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