best options

We (two adults) will be in Japan from 12/2 through 12/18 (16 days total)
We will be in Tokyo from 12/2 through 12/8 then in the Osaka/Kyoto/Nara area until about 12/16 (hotels and daily trips are still in planning stages).
We will arrive back in Tokyo area on 12/16 through our departure on 12/18,

Our question is which pass is best. We will be out of Tokyo for about 9 days.
1) It seems that the JR Rail pass is only good for 7 days costing about $275 pp.; and that a one-way ticket between Kyoto/Osaka and Tokyo is about $140pp, and a 14 day pass is just about $440 (which is just $25 more).
1a) Given out itinerary is it better to purchase a 14 day or a 7 day plus buying add-ons?
1b) What advantages and savings will having a 14 day pass give us in the Tokyo, Osaka, and Kyoto areas if we activated it on 12/3 through 12/17?
2) Are there any legitimate rail/hotel packages between Tokyo and Kyoto and/or Osaka that offer real discounts?
3) Can green car upgrade (to the JR Railpass) be purchased just on the long trip between Tokyo & Osaka/Kyoto? how much is it for just that segment (round trip)?
4) We will have minimal luggage (carry-on & backpack) is it difficult storing them in ordinary class cars for the trip between Tokyo and Osaka and/or Kyoto?
Thank you. We have found your responses to the other questions in the forum very helpful
McVille.