11 days in April (family of 4 seeking ideas)

Konnichi-wa! I'm extremely excited to be taking my family (wife and two daughters, 14 and 10 years old) to Japan the first 2 weeks in April next year. (April 2nd - 13th specifically). After taking the NEX 1-way to Tokyo, and spending 3 - 4 days in Tokyo exploring using the Metro (I've read about the Suica card), I'd like to activate 7 day Japan Rail Passes to visit Yokohama (1 day), Nikko (1 day) and Kyoto (2 days) with the balance spent back in Tokyo.
I'd like to stay in at least two distinct areas of Tokyo (three if possible).

Questions for the forum (with lots of THANK YOUs in advance for your time):

1. Hotels for families: Do families in general reserve 2 separate rooms for a family of four due to room size (this is mainly a budgetary question/concern - In the US, we all fit fine in one room but I am respectful of the fact that Japan is different) Where do you advise I make hotel reservations the easiest/best value? (Is the Toyoko Business hotel chain recommended for my situation?)

2. Can you suggest a realistic itinerary (or maybe point me to some canned itineraries) given the above? We like shopping, museums, ancient architecture, good local food, and meeting new people, are reasonably fit and like to walk. Daughters have never been to a Disney park so Disney Sea was a hope for us. (Yokohama is included because I was an exchange student there 31 years ago and have kept in touch with the family I stayed with - its been a dream of mine to introduce them to my wife and children.)

3. Are there any unique cultural events in Japan this time of year that we might be able to experience?

I'll undoubtedly have lots more questions but again, thank you for your patience with these.

Gooday. I'll just make a few comments since my first trip (8 trips ago) our girls were the same age.

For rooms, it has been rarely that we have had a room that could fit 4, though I think that there are some. We have always taken 2 rooms. It is hard to get adjoining, but we try to get them next to each other or across the hall. Dormy Inn Premium at Shibuya is recommended (by me) - rooms are very reasonable, the breakfast is good and it is a good location, even if you do have a view of a graveyard next to the temple. If you are going to Hakone, the Japanese /western rooms at Lalaca at Gora would easily fit 4. At Kyoto the Japanese rooms at the Westin Miyako (great hotel but a bit out of the way) fit 4 at a pinch, it is also a great setup, similar to a ryokan.

For activities, see if your kids like Miyazaki movies (Totoro etc). If they do, then the Ghibli museum if worth the trip. no rides or anything, but it is a lot of fun. But you need to book in advance.

Consider a trip to Nara as well, about a 1/2 hour from Kyoto.