For the trip to Kyoto, I would recommend seats in the Green Car (non-smoking) 
on the Bullet Train.

In Tokyo, I think that you and your son would enjoy Odaiba - Joypolis. 
http://gojapan.about.com/travel/gojapan/library/photo/bltokyo_odaiba2.htm

I also think that Asakusa would be a fun area to visit. 
http://gojapan.about.com/travel/gojapan/library/weekly/aa021201a.htm?terms=Asa
kusa

I will talk with my wife this evening to see if she has any additional ideas.

Thank you again for lunch.