Just returned from Peru and a trip to Machu Picchu. It was with an organized tour that had included the Galapagos Islands. We drove by bus from Cuszco through the Sacred Valley and picked up the train at a half way point between Machu Picchu and Cuszco. I think it would be fun to take the train the whole way and stay overnight in the village at the base. Although we stayed at the hotel at the site, it was my understanding you would not be able to book there unless you stayed at another Orient Express Hotel. Perhaps the train might qualify as it is owned by Orient Express. Anyway, there are many places to stay in the village at the base and from there you take a bus up in the morning returning in the afternoon. Might even be able to get a guide there if you wished to have someone explain everything to you.