ok, first up you really have to book the Inca Trail in advance. I used SAS and don't have a bad word to say about them. Think they were just above average in cost but everything ran well, porters treated well, good food, nice sites, great guides. Another I have heard good things on is Llama Path. Price was circa US$375 I think.
As for a route to encompass all that.
I would go:
Rio - Iguazu (20 hour bus). I would prob stop somewhere on coast. Would take longer but the Brazillian coast is beautiful. Paraty 3-4 hours south of Rio maybe with Ilha Grande. Then you would need to go to SP and on to Iguazu.
I would spend a few days each side of Iguazu border.
Iguazu - Posades and across to Salta (in Argentina) where you can then enter Bolivia and go to Tupiza. From there you can do a 4 day 4WD trip to the Salt Flats for about US$50 - 80 depends how you haggle.
Then maybe up to Sucre which is ok for outdoor persuits.
On to La Paz. From there you can do things like mountain biking which are excellent and its a good town. Very interesting markets and place to visit.
You can fly from there to Rurrenabaque for about $60 return I think it was (booked 2 days in advance). From there you can spend several days in jungle or go up the river fishing for piranha, swim with pink dolphins/caymen etc. There is a lot of good wildlife on the waters edge. That only cost me about $60 odd for 4 days/3nights all inc.
On to Lake Titicacca/Copacabana and maybe the islands.
Then over to Peru and maybe the uros islands on the lake.
Up to Cuzco and do your MP/Inca Trail thing. Great city again. Brilliant food.
Down to Colca Canyon and on to Nazca.
Short trip to Huacachina to finish with some sun and sand surfing.
The timings of the places you would visit all almost tie in with the times of year I was in them and the weather was generally pretty good.
I don't know Columbia at all sorry.
[ Edit: Edited on 03-Nov-2009, at 07:04 by tricky ]