This is what we did in Dec 2001:
The train is very slow getting out of Cusco because it has to climb steep mountains... the total trip is about 4 and a half hours, and usually requires getting up at the ungodly hour of 5 or 6 am. Instead, we took the train from Ollantaytambo (AKA Ollanta), a village in the Inca Sacred Valled. From Ollanta, the train trip is only 90 minutes long.

You can get to Ollanta from Cusco by bus. We got there by cab (about US$15). They also have shared cabs (called "colectivos"), but they cram in 5 passengers in a station wagon, not comfy, and definitely not private, but costs less than US$2 per person.

From Ollanta we took the Backpacker train (US$10 one way) in the evening. We took it back to Ollanta the next day late in the afternoon. In MP (the town below is called Aguas Calientes) we stayed at the Gringo Bill hotel for $25.

Please note prices may have changed in the last four years....