I was on the Amazon trip in 2007 and never had a problem. I ALWAYS carry Immodium, but never had to use it. When I was there we were able to bring our own wine on the river boat. If you enjoy wine, purchase several bottles in Lima before heading off to the Amazon. The on-board bar ran out early.
I found that I didn't need the bug spray that I had packed. We saw many very interesting insects, but never a mosquito. As for shoes, one pair of sandals and one pair of Lands End water shoes were perfect.
The food on-board was wonderful! How did the kitchen staff do it?
For a book (a mystery!) that takes place on an Amazon river boat, try "Little Tiny Teeth" by Aaron Elkins.