We went to Japan for three weeks in Feb/March this year with our eleven year old DD. I had a thread beforehand which gave us loads of useful advice, so will try and dig that out in a bit.
We got our whole trip organised by Inside Japan, who were amazing, and I could not recommend them too highly, it really helped having not just the bookings made but also hints and tips (like taking small gifts for guides and small hotels). They also organised a couple of half-day guides for us, which really did give us more of an insight. Also, Tokyo is completely overwhelming for the first couple of days, so having someone to help you understand the metro is brilliant! They also pre-booked us into attractions like the Ghibli Museum (which has to be done 3 months in advance) and Universal Studios.
I could write an entire essay here, but do DM me if you want to ask me any questions. I am happy to dig out the hotels we stayed in as well if you want.
We did a slightly longer version of your trip: Tokyo, a couple of days in the countryside round Mt Fujii, Kyoto, Osaka, then back to Tokyo. Probably one of our highlights was staying at two traditional ryokan inns with the onsen baths and eating dinner there, so that is definitely worth doing.
The only thing I would change about your itinerary is to spend a bit more time in Tokyo first then come back for a shorter time at the end - it's a good place to get your bearings as more people speak English there and there is so much to see.
I second the recommendation about the Japan Rail Pass. We had this and it was wonderful - all you need to do is book your seats when you are there.
Agree totally about getting the portable wifi hotspot - it was worth every penny we spent on it, if only for Google Maps. We wouldn't have got anywhere otherwise. Also the luggage forwarding service is brilliant.
We didn't do Disney, but did do Universal in Osaka, which was amazing. You need to get there a good hour before opening time, and then book yourself guaranteed time slots for some of the rides/experiences, then the queues are not too bad. There are English language apps which give you the waiting times, so you can gauge the queues in advance.
Also, allow some time for shopping. Our two favourite shops were Daiso, which is a 100 yen (c.80p) shop but which sells food, tourist souvenirs, household goods, moulds to make bear shaped rice for bento boxes, stationery and much much more, and then Tokyu Hands which is the same sort of thing but more expensive, so if you need a back-up phone battery in the shape of a cat, that's the place. (It turned out that I very much did need one). We bought an entire new suitcase to bring our haul back; I thought we'd bought too much, and then came back and regretted not buying much more.
Also souvenir t-shirts and so on, and other character stuff like Sanrio are really good quality, so we bought quite a bit of that sort of thing. We became rather obsessed with a character called Gudetama, which is an egg with depression issues, who's really popular there and bought loads of that too.
Also, no one has mentioned hotel breakfasts which were a big part of the fun for us. There are always a few Western items on the menu (eggs, sausage, a kind of bacon), but along with them comes rice, miso, savoury dishes, salad, seafood fritters, and much else besides. I gradually realised that most of the greens you will get offered during the day come at breakfast. In the big hotels they serve almost everything - our one in Osaka had a buffet of mini-desserts and I ended up negotiating with DD that she could have macaroons and creme brûlée for breakfast as long as she had a bowl of salad first.
The other thing I would add is that it is amazingly clean, and not so expensive, especially for food, but most of all that everyone there really wants you to have a good time; there's none of the sneeriness about tourists that you can get here. People were so helpful and random strangers on the metro would make sure we were on the right train!