This FKT simply involves going from the Plaza de Armas in Cusco (the cap. city of the province) to the Plaza de Armas in Pisac (the principle town in the Sacred Valley). You can go the other direction, but Cusco is quite a bit higher. Runners can take any route they like, but we'd recommend NOT running on the narrow and winding paved road, frequented by extremely aggressive drivers. There are tons of trails and open country up high and so there are many ways to string a route together, depending on your preference, but you'll have to get up over the high pass between the city and the valley and down into the Valley and then into the Plaza de Pisac.
This is a spectacular area with some very well trodden trails and dirt roads and some tiny animal tracks that peter out into nothing. Have fun!
Very cool! Buzz, Stephanie & I did a similar route back in Jan or Feb of 2004, but opposite direction. We took the bus from Cusco to Pisac to see the famous market, then figured on running back somehow. Buzz had a vague map, but of course no GPS or Strava or anything. We tried to ask for directions but were told "You can't do it". Having got a late start after messing around at the market we didn't know if we would make it back before dark. After a while Stephanie said we should stop and discuss: "We don't know the route, it's late, we don't have flashlights, maybe we should go back?" I looked at Buzz and knew he was thinking exactly what I was thinking: "Perfect". But we very calmly convinced Stephanie that it would be okay, and in fact we got back to Cusco just at dark. Great memories!