I've been to Peru several times. Machu Picchu is very cool . You also want to see Cuzco - in fact you'll likely get to Aguas Calientes (the town at the foot of Machu Picchu) by train from Cuzco. Something else you should try is a jungle excursion on one of the tributaries of the amazon. We did one on the Tambopata (sp?) and it was very cool - nothing like swimming in pirhanna & cayman infested waters

There are lots of travel agencies in Cuzco that you can book this kind of trip with, though I think our reservations were made earlier. I'll see if I can find anything more specific about the place we went - it'll cost you a few extra immunizations, and anti-malarials though. If you're going to do that, start taking the anti-malarials before your trip. They don't agree well with some people (iincluding me) for the first few days. Better at home then on vacation.
I've also been to the Nazca lines, and was somewhat underwhelmed. If you're short on time, that's one that I wouldn't feel to bad about dropping off the itinerary.
I've never had any trouble there. The first few times I was with a native, but the last time I wasn't. I don't speak much spanish at all, but a good number speak english and you can wing it beyond that. Pay attention to where you are and what's going on around you. Try to travel with other people. Don't draw attention to yourself or show/carry alot of money. Normal stuff.