Have you considered flying out of Kansai airport instead of returning to Tokyo? If this is an option I wouldn't bother with a Japan Rail Pass and I'd just buy a one way on the Nozomi train between Tokyo and Kyoto.

Narita is further from the city than Hanaeda and it will take longer to get to than Hanaeda.

You could also fly from Itami to Narita or Haneda for international connection. The cost of including that in you ticket is typically very low. As an afterthought much more costly though.

I researched some more and I think I will go with Haneda. Next question then is should I go straight from there to Kyoto and then come back to Tokyo and fly out. I can get a Cathay package from Hong Kong to Tokyo and add Kyoto on my own. The package is much cheaper than buying flights and hotels separately. Still looking into the possibility of doing one way though... Did not know about Kansai. Will look into it also. Thanks!

I decided to do what was suggested - fly in to Haneda and out of Osaka/Kansai and taking the Nozomi between the two. Have already booked Westin Miyako in Kyoto, but struggling with hotel booking in Tokyo. Would like to stay in Roppongi, and Grand Hyatt was suggested, but it is coming around USD 2000 for 3 nights - a bit much! The Intercontinental ANA is available for about half that price, but nobody seems to talk about it here. Has anybody stayed there? Any feedback? Thanks.

You should fly into HND and out of KIX if at all possible to save you time and money. There are tons of flights KIX-HKG which would save you the train fare and time backtracking to Tokyo. I would fly an open-jaw flight HKG-HND then KIX-HKG. I see lots of cheap flights with this itinerary on www.kayak.com

You can then buy a one-way shinkansen ticket when you get to Tokyo and not worry about buying a JR Pass which would have to be bought in your home country as they do not sell the 7, 14 and 21 day JR Passes in Japan.

There a a few shinkansen tickets and hotel rooms on this site that are pretty good. You can call or email for the one-way pricing or you can take your chances when you get to Tokyo to see what deals a local travel agent(in your hotel lobby) can offer(sometimes have very good deals).

http://www.japanican.com/special/shinkansen/

I have booked rooms with Japanican several times with no problems.

Aloha!