Have you tried calling Star Peru (there is a US # - Florida based IIRC) for connecting flights? Their website won't support it, but in person they are very helpful. I booked a much less complicated itinerary LIM-CUZ-PEM then PEM-CUZ and finally CUZ-LIM for $250 in April.
The downside is they have fewer flights per day so if one is cancelled I may be SOL. That said the only thing I would be *extremely* upset about missing is my Inca Trail hike and that is purposely well cushioned by extra days doing "less important" things.