Would like to another approaching.
15yd aughter, you can leave her alone in Tokyo for 1 or 2 days no problem.
You should tell her to come back to the hotel before 19:00 in the evening,
instead, pls contract with a "rental mobile phone" for her
or if you have "Wi-Fi" terminal such as "iPad","mobile router" will be cheaper.
She can do it in English, such as map, translation, train/bus transfer search, etc by apps.
Allso you can talk to her by voice call apps Skype or.
And don't know what kind of anime or manga she loving,
but in that age "Ghibli" may have graduated already.
(Before that you can not easily book "Ghibli museum")
Also "Cartoon" and "Animation" are different things,
her interest has already shifted to adult world theme's one rather than fantasy and just "cute".
Yr daughter is in trouble separating fr you is that
she cannot say "pleeeease!" when in anime shop also cannot deposit large luggages after shop out.
Managing money also no problem, if you give cash for shopping and eating
with "Suica" or discount tickets for transportations also for convenience stores.
She can understand "money sense" in first two days.
And, do not know when to travel,
but it is also good to make same age Japanese friends on the internet before.
Anyway, first step is let's talk about where the daughter absolutely want to go ASAP,
then check the traveling time by Google map.
Also she can easily go to Kyoto alone by taking a Shinkansen(bullet train).
If taking "Nozomi(fastest Shinkansen name in this section)" fr Tokyo stn,
will be stopping at "Shinagawa(Tokyo)", "Shin-Ykohama", "Nagoya"
next is Kyoto so 3 stops only about 2h20min, so you can eat together if take a early evening train.
https://youtu.be/_K1CuPTKGy0