We are Canadians (couple with a 6 years old) and are planning a Spring Break trip to Tokyo and the Kyoto area for 7 days. We will be in Asia before hand and will be arriving from Singapore. So this trip will be a stopover before we fly back to Calgary. We are thinking of spending the first 2 days in Tokyo and the last 5 days in Kyoto with day trips to surrounding cities. A few questions:

1) What would be some of the must sees in Tokyo and Kyoto area given our times in those two cities? Is the Central Fish Market worth it?

2) Is it worth staying at a Ryokan for the cultural experience such as the Kagaya Ryokan, which is out of the way? Are meals always included for Ryokan stay? Any Ryokan you would recommend in the Kyoto area?

3) We also like to experience the Japanese Hot Spring. Any recommendations?

4) If our departure time from NRT back to Calgary is 4 pm, would it be too risky to leave Kyoto in the morning, say 9:00 am and transfer at Tokyo station with luggages and a six years old for a tran-Pacific flight?

5) As I understand it, a JR Pass is not valid for the express train. Would it put my ability to catch the return flight as per question 4 more at risk?