TDLR: Been there. Get vaccinated/take pills. Take a book. Dont worry about repellent.
2004ish: My ex-girlyfriend and I took a river boat ride down the amazon that lasted a couple of days (maybe a week?). (Roughly the same area you are talking about) When I say boat ride, think old school double-decker river boat where the 1st level was completely packed with cows and other livestock being transfered down river and 95% of the people traveling were locals. The boat looked something like
this We ate what was cooked on the boat, and picked up some tamales wrapped in banana leaves (big ass leaves, probably not bananas) during stops. Luckily I had one of the GRR Martin books with me...you'll want to take something to read
Prior to the 'cruise' I had to meet up with my girlyfriend that had been doing research on some birds out in the middle of the jungle. I got to take a tiny prop plane and fly into the middle of who knows where. (It was a tiny friggin airport...think one room to check in and wait for plane before walking onto the tarmac/field to load up) Once we met up, we had to hitch a ride to get to the nearest river-port-area-thing-place. To get there, we took the longest fucking ride of my life. We rode in what i think was a ford pinto down hours of dirt road. This road had potholes so large that elephants could have gotten lost in them. they were fucking huge and in the middle of the jungle. At one point, we squeezed by a bus that was stuck in one. We ran out of gas twice. After running out the first time, we stopped and gave some of our siphoned gas to another car that had run out of gas...it was the bumpiest fucking ride ever. My neck and head still hurt thinking about it.
Having traveled across parts of Eastern Europe (staying in incredibly rural places) prior to my trip to Peru, I was not prepared for the '3rd world-ness' that was South America.