Travel Plans

Hi there,
Hubs and I will be travelling to Japan for a month in December.
We plan to do Tokyo - Kyoto - Osaka - Kyoto - Hakuba - Tokyo and looking for the best and affordable way to travel.

Questions
1) Does the JR pass allow me to travel this route with ease? Are there specific timings that I would need to follow
2) Do these routes requiring booking the seat?
3) Does booking the seat mean green seat?
4) What is the difference between regular seat and green seat?
5) We will be travelling with 1 medium sized luggage bag and 1 cabin bag. Would we need to book luggage aswell?

I really appreciate your help with our questions.
Thank you!