This is what I’m thinking of:

1. Arrive in Rio and spend about 3-4 days there.
2. Head to Sao Paulo (1 day) or leave to end.
3. Curibita (1 day?) is there anywhere else I can go in Brazil along this route? perhaps a train to Paranagua?
4. Foz de Iguazu and then head over to Argentina side (if time permitted maybe even visit the historic Jesuit mission at San Ignacio. (3-4 days?) – do I have to pay to get to Paraguay for this?
5. Take overnight bus to BA (3-4 days)
6. Take boat to Uruguay (Colonia/Montevideo) (2 days?)

Head back to BA - I got this itinerary from Moon’s Handbook which I like:

7. A morning flight El Calafate will take most of the day. Make an evening excursion to a nearby estancia for an asado. where's the cheapest place to catch the flight from
8. Full-day excursion to the Moreno Glacier, Parque Nacional Los Glaciares.
9. Overland by bus or rental car to the Fitz Roy Sector of Parque Nacional Los Glaciares, with accommodations at the settlement of El Chaltén. With an early arrival time and good weather, you’ll have time for a swift hike to view the glaciated needle of Cerro Torre.
10. Strenuous full-day hike to Laguna de los Tres, with stupendous views of Cerro Fitz Roy. Evening return to El Calafate.
11. Spend a relaxing day at an estancia like the rustic Estancia Nibepo Aike or the more luxurious Hostería Alta Vista, on Estancia Anita.
12. Need help here, I need to fly back to Sao Paulo/Rio to catch the flight home - would i be able to fly directly from here?

I plan to take the buses everywhere except when I’m heading back to Brazil.

Is it possible to visit a town/city in Chile when I’m in Southern Argentina, even as a day trip?

What will the weather be like in Oct/November in El Calafate? Is there anything specific I need to bring for this trip?

It wasn't my intention to visit the Amazonas on this trip. I mostly likely will be back to Brazil at some point and plan to visit Colombia, Venezuela so going to the Amazonas will probably be better then.

Varig flies directly from Toronto to Sao Paulo (and then to Rio) which saves me a lot of time and no changing of flights. The arrival and departure times are also better b/c I will arrive in Rio early afternoon (1pm) and depart from Sao Paulo 10:30pm.

It sounds awfully ambitious, especially as you said you plan to take buses pretty much everywhere. Sounds like you're pretty much going to be stopping long enough to click off some snapshots and then get back on the next bus! You might even fit in a cup of coffee at some point. For example, your "overnight bus" from Iguazu to Buenos Aires is, I believe, 17-18 hours (770 miles). Parts of it you could certainly do quickly - Colonia's a day trip - you take the ferry in the morning, spend 4-5 hours wandering, and take the late ferry back. If you go to Montevideo, it's a four hour trip each way by ferry, so you'd need the two days.

SOME CLARIFICATION

Foz de Iguazu and then head over to Argentina side (if time permitted maybe even visit the historic Jesuit mission at San Ignacio. (3-4 days?) – do I have to pay to get to Paraguay for this?

IF YOU CROSS TO ARG FROM FOZ YOU WILL NOT STEP ON PARAGUAY AND IF YOU WANT TO VISIT THE SAN IGNACIO MISSION YOU SIMPLY TAKE A BUS IN PUERTO IGUAZU (BUS TERMINAL STATION-7 AM) AND YOU WILL BE IN THE RUINS FOUR HOURS LATER.

A VISIT TO THE RUINS WILL TAKE U SOME HOURS. AFTER IT, TAKE A BUS TO POSADAS CAPITAL CITY AND HEAD FOR BUENOS AIRES
(VIA BARILOCHE)

FIND OUT ABOUT THE MOCONA FALLS BEFORE COMING BACK TO BUENOS AIRES. A PLACE WHICH HASNT BEEN DISCOVERED BY TOURISTS AND WORTH 2 DAYS. OR VISIT THE WETLANDS ESTEROS DE IBERA IN THE PROVINCE OF CORRIENTES ON THE WAY TO BUENOS AIRES.
THAT IS THE ADVANTAGE OF BUSSING THE WAY, YOU CAN MAKE STOPS AND VISIT OTHER PLACES


7.- A morning flight El Calafate will take most of the day.
NO, THE FLIGHT WILL TAKE NO MORE THAN 3 HOURS. EL GALPON IS THE ESTANCIA THAT OFFERS THAT EXC.
CALAF CHALTEN TAKES 6 HOURS BY BUS.
TAKE THE 6 AM ONE.
STAY 1 NIGHT IN CHALTEN. AND YES TO HAVE THE FITZ ROY IN FRONT OF YOU IS AMAZING. TREKKING IN CHALTEN IS QUITE AN EXPERIENCE.

IF YOU HAVE TWO EXTRA DAYS IN CALAFATE A GOOD EXC IS TO GO TO TORRES DEL PAINE AND THAT NEEDS 2 DAYS IF YOU WANT TO ENJOY IT.

FROM THE SOUTH TO BRAZIL? FORGET IT.

milla.

I've re-done my itinerary and omitted El Calafate (since that was it was never my original intention to go there).

Toronto > Rio - 4-5 days
Overnight bus to Curtiba - 1 day
Overnight bus to Foz - 2-3 days
St Ignacio > Ibera- 2 days
Overnight bus Buenos Aires - 4-5 days
Ferry to Colonia, Uruguay - 1day
Bus to Montevideo - 1 day
Overnight bus Puerto Alegre - 2 days
Overnight bus Florianpolis - 1-2 day
Overnight bus Sao Paulo > flight Manaus
Manus - 1 day
Jungle - 3days/2nights
Sao Paulo - 1 - 2 days

My itinerary is flexible enough that I can sleep a day or 2 less/more in a place, not relying on any flights until the last few days of my trip when I go to Manaus.

More Questions
1. Should I wait until I get to Manaus to book a trek?
2. Any recommended companies?
3. Anyone been with or heard of Malocas Jungle Lodge?
4. Is it a good idea to wait until I'm in Brazil to book my return flight to Manaus? With Varig it's $518 USD (taxes, return) from Sao>Manaus - is that the best price there is? Can't seem to find anything cheaper.
5. What buses are recommended (safety and price)?

Personal experience says that the two best bus companies for long distance treks in Argentina are La Veloz del Norte and Flechabus. Both have websites you can find easily. The only question will be if either goes between the particular areas you're going to. For some places, you're limited to only one or two bus lines, and they may be, shall we say, less "comodo".

I've revised my itinerary big time and I like this one much more. I've already booked my flight to Sao Paulo...I'm working on my itinerary so I can purchase an TAM Air Pass.

Nov-28 depart Toronto at 10:45pm
Nov-29 Arrive Sao Paulo > Parati
Nov-30 Parati
Dec-01 Parati > Rio
Dec-02 Rio
Dec-03 Rio
Dec-04 Rio
Dec-05 Rio
Dec-06 Rio > Salvador
Dec-07 Salvador
Dec-08 Salvador
Dec-09 Salvador
Dec-10 Salvador > Campo Grande
Dec-11 Pantanal
Dec-12 Pantanal
Dec-13 Pantanal
Dec-14 Pantanal > Campo Grande > Foz
Dec-15 Foz
Dec-16 Foz > Buenos Aires
Dec-17 Buenos Aires
Dec-18 Buenos Aires
Dec-19 Buenos Aires
Dec-20 Buenos Aires
Dec-21 Buenos Aires > El Calafate
Dec-22 Perito Moreno
Dec-23 Upsala Glacier & Onelli Glacier
Dec-24 El Calafate > Buenos Aires
Buenos Aires > Colonia
Dec-25 Colonia
Dec-26 Montevideo
Dec-27 Porto Alegre
Dec-28 Porto Alegre
Dec-29 *floater/extra day*
Dec-30 Sao Pauolo
Dec-31 Home

Any recommendations as to what I can do for:

4.5 days in Rio
4 days in Salvador
4.5 days in Buenos Aires

Is 1 - 1.5 days in Paraty enough or should I just skip it any spend it in Rio or do day trips from Rio?

Anyone have a recommended tour company for glacier tours in El Calafate? Also, I have the afternoon in El Calafate, anything to do there or is that just a stop point for the glaciers? When do most glaciers tours start/end?

Thanks in advance