Hi there!
Here are some answers for you:
I was wondering if I should purchase a JR pass or just purchase my individual tickets on site for taking the Narita Express to the Toyko station then the Shinkansen from the Tokyo station to Kyoto?
For a 9 day trip such as this I recommend:
- [Narita Express + Suica prepaid travel card: single way] for saving money on travel into and around Tokyo
-
7 day Japan Rail Pass to cover travel from Tokyo to Kyoto and back to Narita.
The 7 day pass will be around ¥1450 cheaper than purchasing the return to Kyoto and single to Narita. It will also mean that any further JR travel that you do will be totally free so give you much more flexibility to change your plans while you are in Kyoto. For these reasons I recommend the 7 day pass over normal tickets
I beleive that I can not take the Nozomi with a JR pass but I can take the Hikari, is this correct? If so is there much difference between the Nozomi and the Hikari?
Yes, the JR Pass is not valid on the Nozomi, but is valid on the Hikari class bullet trains. In practice both services use the same rail, trains and reach the same top speeds, but the Hikari service stops at more stations en-route. The Hikari service from Tokyo to Kyoto takes 25mins more than the Nozomi service over the 513km distance. As this difference is small, unless you are under time pressure there is very little variation in the quality of travel.
I want to bet the Green cars for both legs. How do I reserve seats with either option (jr pass or pruchasing individual tickets on site)?
If you want to reserve seats on bullet trains, you can visit the ticket office (with or without a JR Pass) to make your reservation. We have a (blog post on the reservation process](http://www.jrpass.com/blogs/reserving-seats-boarding-the-bullet-train). Please note that although some green car trains do run on the line from Kyoto to Tokyo they are not available on all trains.
Also, is the public transportation in Kyoto (from a hotel to the conference centre) covered by a JRpass?
I'm afraid not - transport within Kyoto is managed by the (non-JR) municipal government. You could consider purchasing individual tickets as needed, or one of the subway/bus passes if you think you'll be doing a lot of travel.
Hope this helps!
