are these lines are covered with the JR Pass?

Hello, me and my mom are going to visit Japan from 07.17 to 07.25, and planning to buy JRP from 07.19 to 07.25. Our destinations are:
-- Tokyo (it would be without JRP) -- Kamakura -- Kyoto -- Nara -- Wakayama/Osaka -- back to Tokyo -- Narita Airport 1) What is the process of changing our orders to our "natural" tickets? Do we need to inform which routes we will be using?
2) As far as I see, there's a route Tokyo-Kamakura by Jokosuka Line. I'm asking so to be sure it is covered by the Pass and if it is needed to reserve the seats, and if we still would like to reserve it, is it needed to go and visit Midori no Mado Guchi ticket offices?
3) How can we travel from Kyoto to Nara by JR Lines? Is it possible not to change in Osaka?
Thank you