Advise for the first visit to Japan

Thanks for your efforts in this website helping others to have a great time in Japan.

We are a family of 2 adults and 7 children (17, 9, 9, 7, 5, 5, 3)

We are planning to arrive To Osaka and departure from Tokyo.

In Osaka, from March 28 till April 4, 2014

we are planning to visit:

Universal studio
Osaka castle
Kids plaza Osaka
Osaka aquarium
Tennoji zoo
Big Bang child center
Imelda joypolis

In Tokyo from 4 to 9 April, 2014

we are planning to visit:

Tokyo Disneyland
Tokyo Disneyland see
Kidzania
Tokyo tower
National children's castle
National science museum
Kokomo nokuni

My questions are:

1. What kind of train we should use inside Osaka and inside Tokyo to visit these place? What is the fares for adults and kids?

2. What would be the fares for adults and kids travelling from Osaka to Tokyo?

3. Is there more suggestion for places for kids that we could visit?

Thanks for your time and efforts