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Get out your computer and head for Google's satellite maps and work your way downstream. You can literally see where towns of any size are and their names. Then try doing some searches on what may be in that town. This will help you answer for yourself several of the questions you asked.
Call the Brazilian Embassy in Colombia and ask what the rules are on crossing the border with a boat you bought in Colombia. They will know better than anyone here.
Assuming you can get good answers from these first two steps, then ask yourself / your companions ... can you read the river, can you fix a boat's motor by yourself, do you love mosquitoes.