Jim,
When we did Machu Pichu prior to our Mariner cruise in January of this year, I would recommend staying in Lima two nights upon arrival before heading to Cuzco. We flew in the early morning to Cuzco and were met by a guide who took us to the Sacred Valley with some interesting stops along the way (Pisac, Cultural farm, Olitambo etc). By doing this, we did not have to go from sea level directly to Cuzco at 11,000 ft, but instead dropped down to the exquisite, beautiful Sacred Valley at 8,000 ft. I loved the sacred valley and wished we had stayed longer than the one night (perhaps two to three). We took the Vista Doma from the Sacred Valley. It was nice. The Hiram Bingham did not pick up from the Sacred Valley stop - only from Cuzco. In Machu Pichu, the train arrival is around noon allowing you time to visit the site with a return the next morning before catching the 3:00p.m. Vista Dome back to Cuzco. There was a lovely 'fashion show' on the train during our return. We stayed in Machu Pichu because we enjoyed wandering the town. After our arrival we spent three nights in Cuzco. By then we were acclimated and could do the tours to the various sites with ease. On one of my tours there were brand new arrivals from Lima who went on a grueling tour. They could barely get through the tour. You will love your trip. We have yet to do the Galapagos. I am envious of your trip.