Early september is still good weather in the mountains so you shouldn't have flight delays, at least because of weather. I recommend Lan or Taca.

The not-to-be-missed sights in Cuzco are the ruins near the city (Sacsayhuaman, Tambomachay, Kenko & Puka Pukará - this is a typical half-day short circuit), plus those within and some churches, like the Cathedral and Koricancha (mix of ruins and monastery).

About Paracas, if you have not driven in Peru before, don't do it. We peruvians drive too wild. Take a bus (Ormeño, Cruz del Sur, Oltursa) or coordinate transport with your hotel. It's about 240km, not less than 3 hours.

You have to take a plane from Ica to Nazca Lines to avoid the bus trip from Pisco/Paracas to Nasca (230km). Ica is 80km from Pisco.

September is still winter and though the winter is not so strong (and this year is even less strong), it's usually cloudy every day in this season. Keep in mind this.Anyway I think it is worth it.