I'd do 6 in Tokyo -- it's huge, and I say this coming from a big city. Even using the very efficient transit system it can take a bit of time to get from one place to another. If you're only doing 2 days at Tokyo Disney I'd try to get one of the Disney hotels so that you get early entry. I wasn't a huge fan of Tokyo
Disneyland Hotel -- I think Mira Costa would be better. For me, it would be worth paying cash for one of the official hotels due to time constraints. I'm going to be in Tokyo in January for 3 days and I'm looking forward to it! I
I'd recommend Himeji castle -- it's an easy train ride from Kyoto and very worthwhile visiting.
Also something that we did that I recommend is hiring a photographer (Flytographer is good) to get some pictures of you and your kids in Kyoto. There are some truly beautiful sites and the photographer can whisk you from one to the other to get some great shots.
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