1. I'd stay in Tokyo for your first night; then when you check out in the morning, ask your hotel to hold your luggage, collect it after your day of sightseeing and then go to your Disney hotel. This will save you time and extra train trips, as Disney is not near any other tourist attractions in Tokyo.
2. In Kyoto, skip Nishiki Market. It's just one street, not a big, expansive market. Yes, it has lots of foodsellers, and yes, it was an interesting place, but if you've got limited time in Kyoto I would spend more time elsewhere. Plus, I can't see your kids enjoying it.
3. Do Gion at night - much more atmospheric, and this gives you more sightseeing time during the day. There's also lots of great restaurants.
4. You won't be able to use the JR Pass once you get to Kyoto. The major public transport in Kyoto is buses, and they can be lengthy trips because of the traffic and because most of the tourist sights are outside the city centre. The only place I took a train to is Fushimi Inari - a sight you definitely should not miss. I think the kids would enjoy it too, especially the fox legend and statues.
5. You should be able to fit in your chosen Kyoto sights and possibly even Fushimi Inari over 1.5 days if you start early (most sights open at 9am) and don't dawdle too much. Be aware that the Sagano train is most popular in autumn because of the beautiful foliage - this will be fading when you arrive (November is peak). The Sagano train is very popular so make sure you book tickets early! I think this is a JR train, so plan ahead and make bookings when you exchange your Pass.
6. You won't be able to make it back to Tokyo by 6 after a day in Hakone, especially if you are including an onsen trip. Hakone is about two hours away! There will also be lines for the Round Course elements as it is popular. If my counting is correct, you'll be there on a Monday, which will be less crowded than the weekend, but still busy. My friend and I went at pretty much the same time last year and there were still plenty of people! And we had a great view of Mt. Fuji from Owakudani ropeway station - I hope you will be as lucky! It is a great day out though, and the Round Course lots of fun. There's also a Le Petit Prince Museum in the main town (need to catch a bus to and from) which the kids might like if they know the book. But if you go there, you'll probably have to skip the onsen.
7. I don't know about the ski resorts. Sorry I can't help you there. But be aware there might not be much snow as it will be so early in winter. You might want to look that up, if you haven't already.
8. When travelling between cities, think about doing the train trips in the evening. You're unlikely to be sightseeing then, and it would save you daylight hours. Plus, the kids can just nap on the train (it always sent me to sleep), especially on the Tokyo-Osaka routes (a very long trip - about 3 hours, longer if you end up on the Kodama). Try and book tickets for these long trips when you exchange your Pass too, to make sure you get seats together. Just a bit more peace of mind and less stress later.
9. Maybe consider staying at the Haneda airport the night before you fly out. Saves you a bit more stress if you miss a train, or the kids hold you up, etc., especially if your plane is in the morning. It'll be a long day doing Hakone and then travelling to the airport, though.
Sounds like you've already got a pretty good trip planned! I hope you have a great time.
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