The best guide I know for around Cusco is a guy called Doug, a friend of mine. He normally does tours for rich folks, but if you talk to him when you´re in town he´ll do a cheap option if there are a few folks going. Me and some friends went to Choquequirao with him last week and it was the best trek I´ve had. He´s very informative and enthusiastic about all things Inca, and loves the countryside as much. There are some places I can recommend in the jungle around Iquitos too, but would have to get my notebookk out for details! Sorry didn´t get back to you earlier, havn´t looked at the site for a while and been busy! Give me a shout if you´d like some names of lodges or organizations around Iquitos, for the Pacaya Samiria for example.
Cheers, take care,
Glenn