Travelling to Japan with a toddler and 3-4 adults

I’m taking a family trip with my parents (3-4 adults depending if my husband takes time off work) and toddler end of May and beginning of June. I will also be 6 months pregnant with my second.
We plan to visit Tokyo, Kyoto and himeji as I have a friend in himeji. For 2 weeks with no more then 5 days in Tokyo.
I am looking for recommendations for EVERYTHING.
Our toddler loves animals, trains, other children and the outdoors but gets overwhelmed in bright and loud places as we live in a tropical island where we live by island time. My mother and I love art and my father and I love history and interesting and comfortable train rides. I personally LOVE Japanese food and the ocean.
Things we would like to see and do
– Teamlab toyko
– Robot restaurant (?)
– hedgehog or other small animal cafe
– eat lots of fresh sushi and sashimi
– visit the deer at Naru
– onsen toddler friendly as they LOVE baths
– I would like to chill being quite pregnant so a spa and pool would be nice for a day or two.
Possible options are
– Harry Potter world in Universal studios
– Ghibli park (myself and toddler love Ghibli)
– DisneySea (toddler loves Moana and Encanto)
– Mount Fuji

Where should we stay?
What should we do?

Thank you in advance for advice. I know taking time out of your day to impart knowledge takes time and energy and my family really appreciate it.

by Awakemamatoto

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