On the route, I would be tempted to switch the order of MP and Cusco. Cusco is much higher than MP and you are likely to enjoy it more if you are more acclimatized to the altitude. Also, Tambo del Inka has its own rail station with trains directly to MP so you would save yourself a lot of time. The train wouldn’t be the Hiram Bingham but the Vistadome trains are very comfortable and travelling from the Sacred Valley to MP is much quicker. Doing this would probably allow you to have only one night at MP (morning train to MP, afternoon exploring MP, overnight, morning for Huyana Picchu if you fancy it and train to Cusco in PM) which might give you an extra day in Lima if you want it.
On hotels, at MP, I would recommend the Sanctuary Lodge mainly because of its location – it is the only place right up by the ruins meaning you can be the last people in the site in the afternoon (magical once the crowds have gone) and pop back easily to your hotel for meals / breaks etc during the day. The only access to the site otherwise is by government run bus (or a very steep hike) which is mayhem. The rooms at the Sanctuary Lodge certainly weren’t glamorous (more like a 4* Hilton) but the location cannot be beaten and the food and drink was good.