Re-worked my 3 week itinerary

My small advice on the middle part of your trip ...
Day 6 Village stroll Ollanta.
Day 7 Visit ruins Ollanta (half day) + other activity of your choice (See Awamaki for options !)
Day 8 Take early train to Aguas Calientes, walk to museum, have a quick picnic lunch, take bus up to Machu Picchu. There, pay for a guide for 1,5 hours. Afterwards eat some fruit in a quiet place of the ruins (Don't leave garbage!). Walk around. Relax. Breath the air. Start taking pictures and enjoy the site emptying. Stay as late as possible. In Aguas Calientes have a small diner. Take a late train out of AC and sleep in Ollanta. This way you will have had 3 nights at an altitude of 2700 meters, preparing you better for Cuzco.
Day 9 Leave early for Cuzco with a private transport. On your way to Cuzco visit two are more of the following (choose a you like): Salinas, Moray, Maras, Chinchero. Should it be Sunday there is a market in Chinchero ;o). Overnight Cuzco.
Day 10 Take a transport (buses are perfect here!) to Pisac early morning. Have a not too late quick lunch in Pisac villagecenter. Track your way back to Cuzco visiting Tambomachay, Pukapukara, Q'enqo, Saqsaywamán. From Saqsaywamán walk down (always better when there's not much oxygen around) into Cuzco until the Plaza de Armas. Ask for directions. If you speak Spanish I can refer you to an excellent guide, one of the few I liked around Cuzco. Overnight Cuzco.
Day 11 Visit the Cuzco city center. Overnight Cuzco.
Day 12 Private transport to Puno, visiting the villages of "La Ruta Barroca del Andino". Small, typical villages with beautiful churches and other things. Not the big WoW, just normal Peruvian small town life, but you will be tired of archeological sites by now, so this is something different. Enjoy the rest of your day in the transport.

I don't know Puno, so I have to stop my advice here. I am only going to repeat: Don't fear the night buses with good companies. You may not sleep, but try it at least one time to have tried it. Go for the luxury seats ! Go for the front seats upstairs. I do take these buses with my almost 70 yo mum! And yes, you lose some sleep and some landscapes but you do win a lot of time.

Happy travels!

Wow thank you for that. I'm trying to figure out the logistics of this piece of the trip and this does help. The suggestion for Cuzco - Pisac to Cuzco day - sounds perfect. My Spanish sort of sucks but I can usually make myself understood eventually.

Will try to come to terms with overnight buses.

You have 3 days for Ollantaytambo. It is a nice scenic town. You can visit the ruins and the granaries and explore the town on day 1. Day 2 you can make a day trip to Chinchero, Moray and the Maras salineras. And maybe indeed look at Awamaki for the third day.

You can go to Aguas Calientes the evening before MP or the morning of. If you go the evening before you can get to MP early. It is often foggy early in the morning but we liked that. If you go later (and the best time to be there is indeed after 2 pm when people start leaving) I would not stay in AC the night before. After MP I would go back to Ollantaytambo as well and the next morning take a minibus or taxi to Cusco. That day visit Cusco. The next day Pisac (consider walking from the top of the ruins to the village so you get to see the amazing temple complex, all downhill) and the ruins north of Cusco.

I have not been to Lake Titicaca but consider an overnight on one of the islands.

You can go from Puno to Chivay (Colca) with 4M Express. You could stay in Chivay or Yanque. Visit the Cruz del Condor. Then take a bus to Arequipa. Or look at the Killawasi Lodge tour:

http://www.killawasilodge.com/tours-detalle-total.php?tou_id=16

If you do go to Arequipa first you can book a 2 day/1 night tour to the Colca Valley in Arequipa.

If you are not that interested in Nazca you can take an overnight bus from Arequipa to Ica and visit Huacachina. Then take a bus from Ica to Paracas (or to Pisco and take a taxi to Paracas from Pisco) for the Ballestas Islands (boat tour at 8 am and 10 am) and the Paracas Reserve. Then it is 4 hours by bus from Paracas to Lima.

Thank you soniaberode. Very helpful. I'm getting things figured out...slowly.

I would also go Puno to Chivay, visit Colca Canyon and than go to Arequipa.
Nazca is great, here is my trip report (point 11).
https://www.tripadvisor.com/ShowTopic-g294311-i818-k9623456-Trip_report_20_days_in_south_Peru_part_2_Colca_to_Lima-Peru.html

I had been thinking it would make sense to spend a couple of nights in Arequipa first, where we could arrange a Colca Canyon tour. If we go to Chivay, would you suggest booking a tour ahead of time that starts from there? We probably don't have time to spend more than one night in Chivay, then an overnight trek and then a couple of nights in Arequipa.

Or is it possible to book a trek a few days ahead of time while we're in Cuzco or Puno?

Contact a few hotels in Chivay, they should be able to book a tour for you, from Chivay to Arequipa. They can also include a bus from Puno. I would contact them in advance.

You mention an overnight trek... do you want to hike down into the canyon? We loved it but going back up is steep. It is possible to rent mules though.

For hiking down into the canyon you have to go to Cabanaconde. You can take a bus there from Chivay. Any hotel in Cabanaconde can help you plan your trek. You can do it on your own like we did or you can go with a guide or take a tour. This website has lots of great information:

http://www.pachamamahome.com/

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