$100 Lima to port (RT). $200ppx for the flight to Cuzco. $699ppx for the train. $200 hotel in Lima, $100 hotel in Cuzco. Under 50% of what HAL is asking for 2.
Flying to Lima to Cuzco is the only way to do it in this amount of time and you will likely take one day to deal with Lima, one day to get to MP and back to Cuzco. Next AM, fly back to Lima, on a bus and you are back on the ship. If you are overweight, physical disabilities, need O2, be prepared. Cuzco is 12k' and MP is 8k'.
Those O2 bottles at Walmart would work well. Most average flat landers have problems just walking around Cuzco. If you have a chance, warm up walking to Sacsahuamán (above).
I don't find rushed trips like that enjoyable. I walked the Inca Trail to MP, would like to do it again, but it was a booger. I had a flight delay so landed late and had to start hiking 15k' passes the next day.