Tokyo to Hiroshima

I am planning my first visit to Japan in mid August and thought I would use a 14 day PR Pass for the following:

1. Tokyo to Kyoto. Stay 5 nights and visit the area and Nara
2. Kyoto to Hiroshima. Stay 1 night
3. Hiroshima to Hida Tikayama. Stay 2 nights
4. Hida Tikayama to Hakone. Stay 2 nights.
5. Hakone to Tokyo.
6. Day trip from Tokyo to Nikko.

I want to spend time absorbing the atmosphere and culture of each place rather than rush about. Is this a sensible itinerary? I wish to avoid strenuous hilly walks as my wife is unable to walk long distances.

Can seats on trains be booked a long time in advance and is there a timetable for each route?