Hi there
I was in Peru one year ago, and it was unbelievably wonderful. The only bad part about my trip was that I was only there for a week.
The altitude was something I was worried about before I left. The day I got there I had a few dizzy spells, but other than that, I was fine. My mom it affected alittle more. Regardless of your level of physical fitness, you will huff and puff more than usual.
We went to Machu Picchu towards the end of my trip so that we would have a few days to acclimatize to the altitude if necessary. Altitude or not, it will take your breath away!
If you are worried about it, give yourself a few extra days, or talk to your doctor. I know my mom brought along a prescription that is suppose to help with the altitude. Or you can partake of the local cure - mate de coca.
If you have any more questions, feel free to PM me and I will help you out if I can!