Mrs. Keba and I went to Peru last summer and it was definitely one of the greatest trips we have ever been on. MY itinerary was:

Day:
1 EWR-LIM. Arrive very late at night
2 Flight to Cuzco and afternoon tour in Cuzco
3 Tour of Ollantaytambo / valley of Incas
4 Trains to and from Macchu Piccu
5 Bus from Cuzco to Puno (about 8 hours)
6 Boat tour on Lake Titikaka, Uros and taquile islands
7 flight to Lima
8/9 two days in Lima

The train from Cuzco to MP took about 4 hours each way. There is some great scenery but it is still a long trip. The Helicopter was our first choice but it was not operating. It was explained to us that it would not be operating again due to environmental reasons but I don’t know if that was BS or not. If it is available I would do it because the flight through the mountains would awesome.

The time we spent in MP was too short because we only allocated one day. If time permits I would definitely stay overnight.

As mentioned above I did not take the train from Cuzco to Puno. On the bus we made a few stops at a cathedral, some Inca ruins and some other places which I cannot recall at the moment.

I rarely travel on tours or packages but for this trip we preplanned everything with a travel agent in FL who specializes in Peru. Each day was customized for us and we had people who met us in each airport.

If you need more info please let me know.

Keba