Tango,
You may be right about the mosquitos being in the lowlands. I know that the mosquitos are not supposed to be an issue in Cuzco, but that Macchu Pichu is a bit lower in elevation. It may be high enough to not be a problem for malaria, but it is definitely in the middle of the jungle and there were lots of creatures biting us there. I'm assuming that the altitude makes it cold enough at night so that you don't have mosquitos.
In any event, carry something with lots of DEET and use it frequently.
Rhinochaser