Hi all,
Just completed the trip and see a bunch of posts asking for details and things like local contacts, price approximations, schedules,etc.
Rather than replying to each post, I write a guide (even includes a map) on how you can do it. Check it out!
http://www.boundlesstraveler.com/how-to-travel-from-ecuador-to-peru-via-the-amazon/
Good luck and have fun!