Suggestions for boy&girl 12 yrs &parents

We are travelling from our home in Australia to Japan on 23rd September and have arranged accommodation for 5 days in Tokyo (Ueno), 7 days in Kyoto (near Kyoto station) and then 2 days back in Tokyo (Shinjuku). There are so many places which sound interesting, but don't know what to choose, and in what order, so we don't have to waste time backtracking. The children and my husband like science, technology and nature, and my husband and I also would love to go to a tea ceremony, kabuki, museums, Himeji Castle and cultural type things (not just temples).
We don't plan to go to Disneyland as we would more like to spend our time seeing things which are distinctly Japanese. We have purchased a 14 day rail pass. Can anyone please make suggestions for an itinerary? And please can someone let me know how to organise going to a tea ceremony?
Thanks so very much!

I would suggest that you consider visiting the Ninja Museum in Iga-Ueno which is outside Kyoto. This website contains details. It is very interesting especially the ninja demo, and the visit dismissed all the myths that we had about ninjas. Certainly worth the side trip.

please have a look at a previous post further down in the list:
"Trip to Japan with Kids
Tokyo 23-ku"
you should find interesting ideas.

I have heard good things about the RiSuPia Museum for teens interested in science and technology -
http://risupia.panasonic.co.jp/en/index.html
though I have not been there myself.

Thanks for the great ideas. I especially love the idea of the Ninja museum which is a bit different from things you see in tourist brochures. And it's interactive which is another bonus.
Thanks so much!