One of the most overlooked things when planning a trip in South America is the travel time and distance between locations. Traveling 3 to 5 weeks starting in Lima and finishing in Rio de Janeiro is possible if you take flights between 1 or 2 destinations.
I myself bused 18 months in South America and have no experience with flights. OneWorld does look like an excellent service. For information about air passes I've found excellent information here.
Some of the attractions you mention such as the Kaieteur Falls, the Galapagos Islands and Noel Kempff National Park are very isolated and you need time to visit them. I have mapped out a possible itinerary. Just use it as a general guideline. Expand it as you see fit.
Possible itinerary
Southern Peru
Bolivia
- La Paz
-
Salar de Uyuni (you can cross the border to San Pedro de Atacama in Chile but there's nothing to do there).
- Rurrenabaque (jungle trip)
Northern Argentina
- Salta + Train of the Clouds
-
Iguazu falls (maybe via Buenos Aires)
Brazil (you'll need a flight to visit the Amazon)