4 weeks itinerary and how to get around Tokyo, Shimoda and Kyoto

Hello. We are a small family of 3 and we are going to spend 4 weeks in Japan in July. We are first timers in Japan and also have a small daughter. We like to take our time to do things and we are happy on not seeing every single temple and sights available. Knowing that here is our itinerary:

8 nights in Tokyo - We will probably get a flat in a central location (shinjuku or shibuya) and go around Tokyo.

10 nights in Shimoda (Izu Peninsula) - We rented a house in front of the beach and planning to surf and relax for all those days. Maybe do 2 or 3 day trips to see something around but not the main reason that we are staying there.

7 nights in Kyoto - We rented a house there too and will explore Kyoto and visit at least Nara and Osaka.

2 nights in Tokyo -

Can I get recommendations on how to go around and what kind of pass we should get? Open to any other tips but we will keep this itinerary.

Thanks for taking the time =)