Let's see...
- Are we trying to do too many sites?Yeah, a bit. But you have chosen the best. I understand you can't stay more days, or changing the award flights is not an option.
- Do I need more time in the Cusco area? I've been in Cusco 5 times, one time it was 12 days (including inca trail), so you know... never enough
.
But seriously.. Pisac Market is within the sacred valley, so that whole tour could be on day 3 and I would avoid Inti Raymi.
Another must is the ruines near Cusco city: Sacsayhuaman (don't miss it), Tambomachay, Qenko y Puka Pukara. You can do it on day 2 afternoon (enough time) but JUST if you acclimate and feel fine. (is closer than sacred valley so it makes sense).
- Is it worth 3 days at Lake Titicaca just to stay at Isla Suasi? You board their boat at 730am in Puno, which means arriving in Puno the night before.
Are the floating islands all that great? Isla Suasi is far from Puno city . It's worth it, but if you want to save time, you can stay at Puno city (not the nicest city but it's more practical to do it), at a Casa Andina Classic or similar hotel, and take a day trip to the floating islands and Taquile island (closer than Suasi), I did it and it's wonderful. And YES floating islans is worth it! (IMHO). The day trip pick you from hotel at 6am aprox, so you must arrange everything anticipated.
Then you can cut one day fro Puno and stay one more in Cusco, that would be my decision. Again, just my opinion.
- Is Colca Canyon worth 2 of our 13 days? I did 2 entire days (2 nights actually) but staying one night is enough. Not sure what you like most, actuall. But if you are looking for landscape, nature, valleys, flora & fauna, Colca is a must.
- Are we shortchanging the rain forest/jungle areas?
I've not been in Puerto M., but in Iquitos. Not sure if 2 days is enough, I would say yes, but I guess you must do more research.
If it's your first time in Peru, I guess the main stops are Cusco and Puno. But again, it depends on what you want to see, what you like most. Cusco is more history, ruines (plus landscape valleys). Puno and Arequipa are more nature, landscapes, valleys, mountains, the lake.
Jungle is.. obviously nature, adventure!, animals!, rivers, HEAT!!!