Treat for daughter :)

Hi, looking at trip to Japan March 2019 and my head is spinning. Wish to get this right as its been my daughters dream trip for so long. Plan to come for 21days.
1. Tokyo for 4 days - have broken plans down to areas and encludes trip to Ghibli museum
2. Kamukura for short stop before onto Hakone for 2days. Plan round trip.
3. Kyoto for 3 days
4. Kayo San for 1 day
5. Back to Tokyo and stop one day before going to Shibu Onsen for one day to see monkeys
6. Finally back to Tokyo for last couple days which includes Anime 2019

I have planned loads for Tokyo but unsure if travel plans sensible and need to look at how long i shall require railcard for.

Any help appreciated :)