I was in Lima, Cuzco, Arequipa, Colca Canyon, and other areas from March - May 2008. If you have any specific questions you can pm me. Plan your trip and where you want to go around how much physical activity you can handle, factoring in some extreme elevation. Iquitos in the jungle is low physical effort, but Cuzco and the mountains can wear you out quickly. Also, you havent said what you want to shoot, city-scapes and street, farmland, people?

If I were to go back, I'd rent a vehicle and shoot desert and sand dunes along the coast for a few days.

Getting around - fly if you have the money, esp. if you only have 7 days. I took a couple of 25 hour bus rides and hitchhiked, saw some things but suffered greatly along the way. Lower cost buses get robbed at gunpoint. Add 25-50% on to any stated bus time.

Lima is a great place for street shooting, the public buses offer a lot, and wandering for a few days is really fun, lots of people working in garages open to the street, or on the sidewalk. Its also large enough to easily fill 5 days, more if you take a bus to the outskirts of town. A very gritty city.

Arequipa is comparatively very quiet. Much smaller, not nearly as many people on the streets, but fun to walk. Hiking in the area is amazing, but you need to be very fit and prepared. Otherwise the snow-topped mountains can provide some great backgrounds. Much less soot in the air, clear sky. I paid $3 for a room in the city one night, bad idea.

Cuzco - I ran out of stuff to shoot after 2 days. Heresy say some, but i'm not into all the polish for the tourists and the knick-knack shops lining the streets. Wandering the alleys at night gave me some good shots, wish I had a better camera to handle it though. I lost 15 pounds here (normally 150lbs) from altitude/food sickness. Thought I could die.

Chivay - You didn't mention it, but I think its the best area for photographers to hang out, and a place that constantly put a smile on my face. Many day trips from here to the smaller towns, accessible by public vans. Its on the way to Colca Canyon, so there are tourist things, but the smaller towns are mostly free of foreigners. If you hired a guide with a car for a few days it could really pay off, especially if you have a low fitness level. Towns in the valleys are surrounded by 5,000m-6,000M snow capped peaks. There are great hot springs to sit in, old rope bridges just like the cartoons. The farmland is wonderful to wander. Amazing irrigation system, and good people. I spoke with a lot of locals who were very interested with me, asking where I was from (USA), and not knowing where the USA was on the map, how big it was, or who the president was, the wars in Iraq, and the list goes on. You could skip Cruz del Condor having so much fun in the other areas. Also, April was the low tourist season there, no idea why, and many of the hotels (hostels really) were closed. I stayed in a local person's house for $5 one night after I found the 1 open hostel was full.
I met a woman in Arequipa from Yanque (great town near Chivay) and she gave me tons of information about who to talk to and how to travel the area, drew maps for me and so on. I have no idea how to obtain this information through the internet.

Sorry for rambling.