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Long Ecuador, Peru and Bolivia trip planning- help please!

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I have now booked flights for a long trip to South America, flying into Quito and out of Lima. On our last trip to South America we very much made it up as we went along. as a result, i feel we missed out a lot. i dont plan to make the same mistake this time. Our outline plan is to spend the first few months in Ecuador. We have booked a room for the first two months at the South America Explorers Club in Quito. We plan to use this as a base for exploring the northern half of the country and to take an intensive Spanish language course before exploring the south of the country.

We then plan to move on down through Peru revisiting some of the places we have been before ( e.g. Cusco and the Sacred Valley etc.) and some we have not, before crossing into Bolivia via Lake Titicaca. After exploring Bolivia, with maybe a side trip into NW Argentina, the plan is to move back up through Peru for our flight back to the UK from Lima.

I am sure I will be back seeking much advice and many opinions, but for the moment here are few initial questions;

1.Does anyone have any experience of crossing from Ecuador to Peru via the Amazon Basin? The only route I can find is from Coca to Iquitos via the Rio Napo, a trip of some 800km, mostly by riverboat. Anyone taken this route or have other suggestions?

2. If we cannot sort out the above route, any suggestions for trips into the Amazon? Is this best done from Ecuador, Peru or Bolivia.

3.How easy is it to cross into NW Argentina from Bolivia?

4. Any suggestions for routes for this type of trip, or websites where I can find some suggestions?

5. Any suggestions for highlights in each of of the three countries? Particularly out of the way or unusual experiences, The more suggestions the better!

6.Recommendations for Spanish schools in Quito.

For background, this will be a budget trip, staying in hostals, B & Bs and travelling by public transport. Any suggestions for great (cheap!) places to stay would be welcomed
Any help would be much appreciated!

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