Dude,
Indeed like the others have mentioned your itinerary looks really horrible, unless it is really about ticking as many boxes as possible. You are planning to go to Tokyo and Kyoto, without actually even seeing the places. Do yourself a favour and plan 4 days in Tokyo and 5 days in Kyoto and cover some of the places mentioned from there as side trips. Also plan your sightseeing by clustering sights that are close by. Himeji and bamboo forest on the same day do not make sense as you will pass by 100+ sights in between.
For Kyoto:
- Download the tourist bus map (e.g.
http://youinjapan.net/maps/kyoto_maps.php), study it and look up on this site all the 3 star sights listed under Kyoto on this website. Plan your trip to hit multiple sights that are close by each other. Get all day passes for your entire family for each day you spend in Kyoto.
- Do not miss some of the great sights like Fushimi Inari, Kyomizu Dera, Nijo Castle, Kinkaku-ji, Ginkaku-ji. - Consider Nara as a side trip, which is great with amazing temples and the deer park.
- Osaka is also close by as a side trip, which is worth spending an evening at Namba / Dotonbori. Maybe good to close off a day after spending the morning and early afternoon around Himeji. I definitely think Himeji castle is worth a visit.
For Tokyo:
- For your kid Akihabara may be nice for your kid with the different arcades, although 4 year old may be a bit young.
- Do not miss out on Shibuya and Shinjuku after it gets dark . Also has some good shopping areas. During day time the Shinjuku Gyoen (park) is also nice to have some quiet time. Not sure how it is during winter, but in spring it was really nice.
- Not sure what you plan to see and do in Hakone. I experienced it to be a bit of a rush to do the round trip in one day. It was fun, but if I had to choose between Hakone and Nikko for side trips the latter would be my definite choice.
-Covering both Disney theme parks in one day is less theme park time for your kid as you spend a lot of time entering/travelling/exiting parks. It's up to you but I would pick one.