JR Pass Coverage

Hi,
We're looking at getting the 7 day pass. We're starting in Yokohama after a Princess Cruise in mid April and will proceed to Kyoto for 3 nites with a side day trip to Osaka. From Kyoto we proceed to Tokyo staying near Shinjuku station for 6 nites. We were told to take the Hikari Shinkansen train on both legs. I understand the Kyoto- Shinjuku leg has a stop and requires a transfer before getting to Shinjuku. Will there be additional charges and how far is the transfer train from the Shinkansen track? Secondly, can we upgrade to a Green car on one or both the Yokohama-Kyoto or Kyoto-Shinjuku trip and how much would it cost? Finally, is there a luggage shipping service in any of the train station. We plan to ship our luggage from Shin Yokohama to our hotel in Shinjuku for delivery in 4 days.

Thanks much.
Roland C