MP and Sacred Valley Itinerary Advise

To avoid altitude sickness you should go from Cusco to Ollantaytambo on day 1. With 3 days in Ollantaytambo you have time for the Ollantaytambo ruins and granaries, maybe a day hike, a day for Chinchero, Moray and the Maras salineras... Urubamba is not really that interesting but I hear Museo Inkariy is worth a visit.
For Moray and the Maras salineras your options are: a taxi tour, a horseback riding tour or hike (that is what we did).

I would spend only one night in Aguas Calientes. After MP take a train back to Ollantaytambo (more departures and usually cheaper than trains to Cusco). That way you can also leave most of your luggage at your hotel in Ollantaytambo. Then take a minibus or taxi to Cusco.

I have not done the Rainbow Mountain hike so I can't comment on that. For the other two days: one day for Cusco and one day for Pisac (take a minibus or taxi from Cusco to Pisac and walk down from the top of the ruins to the village so you get to see the amazing temple complex) and the ruins north of Cusco (we walked from Tambomachay to Sacsayhuaman and back to Cusco but you can of course also take a taxi or flag down a bus between Puka Pukara and Q'enqo).

You can buy train tickets online (Peru Rail or Inca Rail) and you can check availability and buy MP + MP Montana tickets here:

http://www.machupicchu.gob.pe/

Like Sonia said, go to Ollanta on first day.
And I would not stay in Aquas Calientes. Take an early train in and a late train out, sleeping in Ollanta.

Thank you both for the recommendations, those suggestions make sense! I'll make some adjustments to our itinerary.

Beyond the sites that I have listed above, is there anything else I should make sure that we see? Just for reference, my father is big into inca history and my mother enjoys the outdoor / nature / beautiful views etc.

Thank you again for all the help and suggestions!

cheers,
RQ

South Valley is also very nice: Andahuillas (beautiful painted church), Tipon (Inka ruins) and Pikillacta (preinkan Wari (Huari) ruins of a huge town). I went with a tour (booked a day before in Cusco) but you can also use buses and collectivos.

Try and find a good guide to accompany you to the archeological sites. Try someone for one site or one day and decide if he is worth your money. Most guides just studied tourism and aren't all that knowledgable, certainly not to a degree to keep "some really interested" like your father "really interested" for more days. I know an anthropologist who made for an incredible guide but he only speaks Spanish.

Let me have a try at your itinerary.

Day 1 / Pick up folks from airport. Take a taxi to, relax and sleep in Ollanta. If time allows stroll through the village.
Day 2 / Visit ruins + activity (google Awamaki) and sleep Ollanta.
Day 3 / Go to MP, sleep Ollanta.
Day 4 / When leaving Ollanta for Cuzco take an early private transport and visit Maras, Moray, and Chinchero on your way. Allow for some relax to get used to the altitude. Sleep Cuzco. Once the sun sets Cuzco gets really cold, bring warm clothes.
Day 5 / Explore Cuzco. Sleep Cuzco.
Day 6 / Early morning go to Pisac, and on your way back visit Tampumachay, Puca Pucará, Qenko, Sacsayhuaman and from this last site walk down until the city center of Cuzco.
Day 7 / When you are bored of the Inca sites, you can do this "rutadelbarrocoandino.com". Easily done in one day from Cuzco, with public transport and a little bit of Spanish. // Not familiar with rainbow mountain: 11 hours walking at high altitude?
Day 8 / Various options??? An extra night in Ollanta on day 4? Only if you have a good activity planned. / Further afield, possibly not worth your while, is the Saywite Stone (direction Abancay). It should be more or less 3 hours from Cuzco. / Want to walk? From Chinchero you can walk downhill down to Urubamba. Allow a lot of time. Take care of the herd of dogs down in the valley. / Museums in Cuzco /...
Day 9 / Parents leave.

Thank you again for the excellent recommendations! Good call on the guide - I'm going to do some additional research to try to find a quality one.

Muchas Gracias!

RQ

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