Nick,

Having just done my 1M, the only very suspicious customs/immigration officials were in the USA - and this was even BEFORE I started my journey. Most S.Amer immigrations didn't really seem to care.

In Quito and GYE you don't pay the tax (I did the ACES one day return from Lima), and got stranded in GYE), but no chance of avoiding in Lima - 12 soles for domestic (or Cuzco for that matter). In Lima, I'd suggest a hotel closer to the airport - downtown Lima isn't the nicest place to be at night - even in a cab.
In GYE I got bored - everything was closed on the Sunday I got stranded - I just sort of wandered around. The riverfront is mildy okay (for about 20 minutes), and there are a few museums.

Enjoy
Henk