Yes, the Tokaido shinkansen leaves from Tokyo to Osaka, and the first stop is actually Shinagawa eki. If you're planning to take the Tokaido sen bound to Shin-Osaka (and the Hikari you've choosen is one of those), every train leaving from Tokyo will stop there, so it would be indeed the best choice.
Shinagawa eki has a very simple structure, and there is a train coming from Narita (I don't remember the name of the line, but it has a small plane as its logo...) that stops just a few platforms away from the shinkansen platforms.

That makes real sense. I always thought the next stop was Yokohama... Maybe because I usually took Nozomi,

Thank Cyclamen for your recommendation to Shinagawa station.
I think I will choose to get off there if I stick with my current itinerary.
Though it IS a very TIGHT first night in Japan and 20.06 Hikari #389 is the last Hikari of the day, which means if something goes wrong and I don't catch that one I will be screwed. So from that perspective, I may not buy the JR Pass, just buy the regular ticket and find a coupon shop in Kyoto for a discounted ticket back from Kyoto to Tokyo.

It seems Nozomi stops in Shinagawa too :)
http://www.japanrail.com/pdf/Timetable1-west.pdf

I must have always been napping! :D

I bet you were:)

Thanks for the great information. Just got one response back from a Japanese consolidator.

-Airline: Japan Airlines
-Airfare: $1089.00 including tax/fee
-Travel Dates: 10/26-----11/2----11/20
-JFK----NRT---ITM/KIX-----PVG/PVG---NRT----JFK

I think the price is not bad at all, and most likely I will take this plan.

- Oct.26 Depart JFK 13.20
- Oct.27 Arrive NRT 16.20
- Oct.27 Depart NRT 18.25
- Oct.27 Arrive ITM 19.45
- Oct.27 Take limousine to KYOTO
- Nov.2 Take the train from Kyoto to KIX
- Nov.2 Depart KIX 10.35
- Nov.2 Arrive PVG 12.15

Some questions for Japan Airline service. Do I need to take care of the baggage at NRT or ITM in this case? Is the service and food good?

Is anyone a member of the JAL Mileage Bank? Any usage for that? I am an infrequent flyer (usually one RT to China and a few domestic trips in US, less than 30,000 miles a year) and not familiar with those mileage program. I currently only have 25,000miles in UA Mileage Plus.
So should I put the mileage into JAL Mileage Bank or not?
I heard JAL became a member of the One-World program earlier this year.

Thanks.