I am sorry to jump in so late.
The more classic way to do your tour would be to do it the other way around: Lima - Southern Coast - Arequipa - Ollantaytambo - Cuzco - Puerto Maldonado - Lima. This way you lower the risk of altitude sickness, because you would be getting used to some altitude for already 4 days in Arequipa / Cañon del Colca. I did it this way with my 64yo mother and we were just fine. To further avoid altitude sickness we went from Arequipa, passing through Cuzco, to Ollantaytambo. And afterwards to Cuzco. The going up in steps technique I have done with my mum in several high altitude countries. And although altitude sickness is never predictable, science does show that age and being female increases the chance of getting it. And going up in steps sleeping several nights at intermediate altitudes lowers the risk. Take into account that if anyone of you gets altitude sickness in a bad way you, by doctors order, will have to go to a lower altitude for several days / up to a week. This happened to my aunt in the past.
Other advice I can give you:
- Leave Lima for the end of your trip. 2 - 3 Full days is sufficient to visit the historic center, Barranco, Miraflores and go one night to Parque de las Aguas. Leave Lima after your first half night sleep, but give 1 day flexibility to your program in the first week in case your luggage doesn't arrive with you.
- I didn't go to Puno. We already visited it in Bolivia.
- We visited Machu Picchu in one day from Ollantaytambo (early and late train). This way you avoid overspending in tourist trap Aguas Calientes, which I didn't like that much anyway. And you don't need to move hotel. The disadvantage is that you won't be able to climb Wayna Picchu (Not 100% sure about this). Also, we visited MP itself in the afternoon. The light is beautiful an the big tour companies are leaving the site in the afternoon making it slightly more tranquil. I was happy with my decision to do it like that.
- Although I understand about not sleeping in a bus and wanting to see the landscapes, there are really comfortable buses with just 3 seats per row, so you get kind of a business seat, and traveling at night will save you money and time on a short trip. We took a nightbus from Arequipa to Cuzco and I loved it. I was in the front seats (reserve well in advance) of the upper level and enjoyed watching the "night life" along the road. Of course I got to Ollantaytambo totally wasted :o).
Enjoy your trip !
Grtz,
Peter