Which pass is best?

My family of 3 (two adults, one 16 year old) will be travelling to Japan next March (mid to end of March).

Day 1: Arrive Tokyo (Narita) staying in Shinjuku
Day 2: Tour Tokyo (Shinjuku and Asakusa)
Day 3: Tour Tokyo (Shibuya and Akihabara)
Day 4: Tour Tokayo (Harajuku and Ikebukuro). Then Travel to Disney.
Day 5: Disney
Day 6: Disney
Day 7: Take train from Disney to Kyoto
Day 8: Tour around Kyoto (haven't decided on exact plans yet)
Day 9: Tour around Kyoto
Day 10: Leave Kyoto. Take train to Hiroshima. Visit Hiroshima for the day. Take train to Osaka, stay the night in Osaka.
Day 11: Universal
Day 12: See a bit of Universal and then take the train back to Tokyo. Staying in Ginza.
Day 13: Tour Tokyo (Ginza etc.)
Day 14: Tour Tokyo
Day 15: 1/2 day to do last minute things in Tokyo then take train to Narita and fly home.

1.Can you tell me if it is better to get a regional pass for the portion of our trip when we are in Kyoto, Hiroshima, and Osaka? And if so, which one? Or is a 7 day JR Pass worth it?

1. If the 7 day JR Pass doesn't include the Nizomi train, what train can we take? What is the difference between the two? Is there another train that is included in the JR pass that makes the 7 JR pass worth it?

2. If the regional pass doesn't include a train between Kyoto and Osaka, what train do we take? What is the difference?

Overall is it better for us to pay for each train individually? Or is there a pass that would provide us a discount?

1. Do we need to prebook the bullet trains?
2. Do we need to prebook the train from Narita to Shinjuku when we first arrive? What happens if we are delayed and miss the train we booked?

Thank you!