I took my (young adult) son three years ago. He enjoyed seeing places he’d seen in video games and in manga. He could pronounce lots of place names I couldn’t pronounce. 
We spent an afternoon in the akihabara district, which was pretty weird. We also went to an enormous Pokemon shop, where there were dozens of different plush pikachus, for instance.
If she’s into manga, another place to consider in Kyoto, is the Manga Museum they have there. Lots of manga, and most of it can be taken off the shelf and read. Someone really into manga could probably spend a whole day there, easy.
Kyoto is a good spot to consider for a stay of at least a few days. It’s really a mix of everything you might want from Japan - just loads of ancient temples, at least one castle, modern buildings, a decent subway, and lots of cool bars and restaurants. And it’s not as big or busy as Tokyo, so getting around it is a bit less intimidating for people who don’t really speak the language.
But even not speaking Japanese isn’t a deal breaker. I spent most of a day exploring Tokyo on my own when I visited with friends about 10 years ago. Everywhere I went, when I needed help to find my way along, there was someone around who could speak enough English to help me. These days, with things like Google Translate, it can only be easier.
Or taken off the shelf and looked at, given that his daughter probably can’t read Japanese. The gachapon machines would probably be a big hit, though.
If anyone in your family is taking prescription amphetamines, don’t go. You will either be a criminal or have a miserable time because of not being on the medication. I don’t know the likelihood of you being caught, but all amphetamines are illegal for all purposes.
https://jp.usembassy.gov/u-s-citizen-services/doctors/importing-medication/
“Japanese physicians can often prescribe similar, but not identical, substitutes to medicines available in the U.S.”
I tried Ritalin before Adderall. It was awesome for one day, but the lethargy returned the next. I could survive an entire trip on it (I medically don’t need a stimulant - laying in bed all day won’t kill me, and didn’t kill me for the several years I did it), but it wouldn’t be fun.
As much as I love Japan, I’ll love it from afar until it changes its stance on prescription amphetamines for personal use. You’d think bringing a supply equal to your length of stay and a doctor’s note would be enough to make them realize you’re not bringing it in to sell on the street, but they simply don’t care about the humanitarian impact of their draconian drug laws.
If the words of Japanese you know are “So(u) desu ne” you can probably blend in well enough. Won’t get you much information, but if you say it like everyone else does (half the time they start a response to someone, I’d say) they might think you actually know more Japanese than you do.
Kyoto is the best place to visit during Spring. You have to check details about when the cherry blossoms are in full bloom in the area. If your kids like anime, there are lots of places to visit in Tokyo. There’s this J-World Tokyo in Sunshine City Mall in Toshima that includes popular characters from anime like Naruto, One Piece, Bleach. Don’t miss out Akihabara on the list, this is the best place to get your kids’ anime and game related merchandise. Try to visit Skytree as well because they offer seasonal cafe that changes the themes (it was a Kirby cafe the last time I visited). Check the Pokemon center as well, I think everyone likes it. Spend a whole day on Disneyland and DisneySea. Lastly, you don’t have to know a lot of Japanese words. A lot of pamphlets are available at the train stations, convenience stores, parks that are provided for free. These pamphlets can help you with basic city information such as what to do and where to eat. Japanese people are courteous to tourist and they can go an extra mile to provide great service.
Right about now, and the next two weeks.
BTW - It’s a new era in Japan! Goodbye Heisei 平成 and hello Reiwa 令和
Tokyo is amazing and there is an infinite amount of stuff to do. Kyoto and Osaka are also a lot of fun but there’s just so much in Tokyo, especially for your first time, I wouldn’t hesitate to spend the entire vacation there.
I know you say “Spring 2020” which is a good time, don’t let that drift too late because summer in Tokyo can be rather unpleasant plus all of the Olympics stuff may have an impact on your travel plans (including associated cost).
Due to school, we don’t have a lot of options. It’s either March break, which is likely too early, or July. Whaddya gonna do? I don’t think her scholastic performance merits taking that much time off in May.
The Olympics are the second and third week of August, so early July might well be the calm before the storm. It’ll be hot, I guess, but a hot summer day is nice. The average July high is 27C, which isn’t that bad; days of 27 with humidity are common here.
Perfect! You’ve probably already saved a good amount of money. 
My impression of restaurants in Japan (in terms of price versus quality of food) was that they’re somewhere between wow-that’s-cheap and still-pretty-damn-reasonable, with one outlier: a pastrami sandwich in downtown Tokyo. (It was an excellent sandwich, but I fet like a sucker eating it - it was like $23. But I was hungry!)
You guys have time, I would work on some basic sentences and phrases. Japanese are pretty friendly and will usually answer questions.
Just even survival Japanese such as “where is such and such.” Japanese pronunication is quite simple and easy to understand.
Sumimasen biru kudasai?
Sumimasen toire wa doko desu ka?
That got me through.
Then again my ex was a native Japanese speaker so you may want to brush up a bit more.
One leads to the other…
They might even meet Yan over there!
Based on limited experience (one 2-week visit some 25 years ago), my advice would be to prefer traditional inns to hotels.
Restaurant food can be very good value - look for small places with food “models” displayed. When it comes time to order, you can simply point to the model of the dish you prefer; what you receive will look exactly like the model.
a friend told me about Fox island. it sounds really cool but I think your really have to want to go there as it is not easy to get to. “Opened in 1990 and located in Miyagi Prefecture, Zao Fox Village” is a sanctuary home to over a hundred free-roaming foxes, including the silver fox and the platinum fox as well as the Japanese red fox. You can get close to the animals, so in that regards, the fox village is kind of like cat island or bunny island."
Definitely check out Teamlab: Borderless when you’re in Tokyo. It’s easily one of the coolest art exhibits that I’ve ever seen - and will probably be an Instagram gold-mine for your daughter, if she’s into that.
A little video guide.
Japan has a thing for animal havens where you can be surrounded by them. I’ve been to Iwatayama Monkey Park in Kyoto, which was pretty entertaining, and there are other monkey parks as well. And as you’ve noted, there’s:
There are very few restaurants in Japan that don’t have a display of fake food out front:
This is great for tourists who don’t speak Japanese, as they’ll have a pretty good idea of what they’re ordering, at least as far as general appearance. If you feel like taking souvenirs home, visit Maizuru, an outlet run by one of the major manufacturers of plastic display food. You can get anything from cell phone trinkets up to expensive whole-plate displays. It’s a convenient walk over from Senso-ji, and the street it’s on - Kappabashi Dori - has blocks and blocks of stores selling kitchen/restaurant wares.
Another interesting food-related thing to check out is department store basements, which typically host counters selling tons of deli-type food - anything from sushi to potato salad to desserts. The selection is huge and top-notch in quality. I think most locals take this stuff home or to work, but at Mitsukoshi in Ginza, you can buy stuff and take it up to the 11th (I think) floor, where there’s an outdoor patio and garden with tables, chairs, and trash cans, so you can eat what you just bough there.
That last point - trash cans - is important. After Aum Shinrikyo carried out their sarin attack on Tokyo subways in '95, people suddenly got worried that miscreants could hide stuff in public trash cans, so they got rid of damn near all of them. If you generate trash during the day, you’re probably going to be carrying it with you for a few hours before you find some place you can get rid of it.
Tokyu Hands is an amazing store. There are several different sizes; the largest ones carry everything under the sun, ranging from kitchen wares to sporting goods to tools to hobby/craft supplies to stationery. The biggest one I’ve seen is just east of Ikebukuro Station in Tokyo; if you’re in Osaka, you can also check out the one on the south side of Osaka Station (~11th floor of Daimaru department store building), or near Shinsaibashi Station. Other Tokyu Hands stores are smaller and don’t carry quite the same amazing array of stuff.