Hi there,
Here are some answers!
what is a JR PASS (Oridinary) ?
The Japan Rail Pass is a unlimited travel pass available to tourists that allows free travel on all JR lines across Japan, including many of the shinkansen bullet trains (the Nozomi and Mizuho are unavailable). You can find a video explaining more here, and full details on validity here.
What does it include (underground (all lines)/buses (round tokyo) bullet trains to hakone and Kyoto?
The JR Pass includes all JR lines and most Buses (see validity link above for full list). There is a good JR service around Tokyo (map for reference, however as the underground services are mainly non-JR you will need to purchase tickets for this. The JR Pass will cover travel by Hikari shinkansen to Odawara (Hakone stop) and Kyoto.
is is realistic to go from Kyoto to Nara for the day and is it worth it?
This would not be a problem, taking 45mins - here's a sample itinerary for you.
what would people recomend to see?
The main sight in Nara is the Daibutsu at Todai-ji in Nara, however I really recommend you pick up a guidebook to get the most out of the place as there is simply so much to see/do.
we want to see the fish market/marina on our last morning can anyone advise how far it is to Narita airport and is it viable to take luggage?
For Tsukiji fish market you'll need to be there very early to see it at it's best (4-5am is good). There is only access via a small metro station and it is very unsuitable to luggage/tourists inside the market.
I recommend that you leave your main luggage in a luggage locker at Tokyo station the night before you go to the market and then take a day bag with you to the market. Once you are finished at the market you can return to Tokyo station, retrieve your luggage, and board the Narita Express to Narita.
You can look up precise train timetables and costs at the Hyperdia travel planning website and learn how to use Hyperdia for JR Pass holders through our video blog.
Hope this helps!