Choquequirao is a enigmatic ruined Inca city even less accessible than Machu Picchu. In 2005, we had the Choquequirao ruins to ourselves in the late afternoon.
One day it will draw hordes of tourists but for now it is still little visited. The ultimate itinerary is to hike to Choquequirao and continue to Machu Picchu via Aguas Calientes.
As of this date, no guidebook details the long route, 7-days minimum. Guide and pack animals recommended.
If you are looking for an alternative to the over-popular Inca Trail, check out:
besthike.com 
INKA ALTITUDE is the best Local Company for Choquequirao trek , You can find more info: http://www.inkaltitude.com/choquequirao-to-machu-picchu-8-days-7-nights.html