Tokyo to Kyoto

Hi

We are travelling to Japan in July/August (6 nights in total). We arrive at Haneda airport early on the first morning. We are yet to finalise our itinerary but are thinking of spending 2 nights in Tokyo, 2 nights in Kyoto and finishing back up with 2 more nights in Tokyo. We have 3 and 5 year old daughters too. I have a number of questions:

1: Can we use the JR pass between Haneda airport and Tokyo?

2: Do we need a JR pass for our girls?

3: Will we be able to use the JR pass between Tokyo and Kyoto?

Thank you.