Should I get the 21 day ordinary JRP?

Hi there,

What Pass to get? For your itinerary I think a 14-day Pass with the Suica + Nex and Hakone Pass will be the most economic option.
You can use the Narita Express package to travel to Tokyo, than use your JR-Pass to travel all the long distance parts by Shinkansen and finally buy a Hakone pass with access to Shinjuku, Tokyo.

You can find more about the Hakone Free Pass here

Going Green? In general I think there are two reasons why to take a Green Pass over a normal one. The first is you want to travel in extra Peace and quiet, the other is that during periods of frequent travel, such as national holidays it may be hard to get a seat.

You will be traveling one day during Golden Week, which is a very busy period but you can make seat reservations the moment you are in Japan and have exchanged your JR Pass. If you plan ahead a little and do this on the first day that you arrive, than I don't think you will have a problem.

Hope this helps,
Daniel

Thank you very much for all your help!