Hello Daniel-San, thanks in advance, your forum and reverts are quite helpful!

Hi there,

Thank you for your praise - it's definitely welcome :)

Now, let's head to your questions.
a.) Is this your first time coming to Japan? A popular first time itinerary is Tokyo - Kyoto, Osaka (and optionally Hiroshima&Miyajima). This route will already pay for the JR Pass and personally I think these cities are the best as well for a first time visit. To get a good feel of each city, you could do something like:

Oct 9th - Arrival in Japan, stay in Tokyo and recover a little from flying.
Oct 10th - Explore Tokyo
Oct 11th - Travel + Explore Kyoto
Oct 12th - Kyoto
Oct 13th - Osaka
Oct 14th - back to Tokyo
Oct 15th - Tokyo + flight from HND.

In a way it is quite basic but it is well balanced and will give you enough time to see each city. If you are not too interested in cities, then you could swap Osaka with Hiroshima.

b and c.) Generally it is fine to make seat reservations on the day of travel, to be sure you could do it 1-2 days in advance and you will never have a problem during normal days (2-4 days are recommended during national holidays). You can of course take a 2nd class seat for free but since you've paid for Green Class, you will want to ride in Green Class :)

d.) You are allowed to full size suitcases to bring on the Shinkansen, this is not enforced though and not an exact limit.

e.) You can take the Narita Express train directly between Narita Airport - Tokyo using the JR Pass. To Haneda from Tokyo. Take the JR Yamanote line to Hamamatsucho, from there you can use the Tokyo Monorail for free with the JR Pass to Haneda.

Hope this helps, let me know if you have any follow-up questions.

Kind regards,
Daniel