US-Japan-China-US trip

Hi,

I am going to Kyoto, Japan at the end of this October for a one-week conference, and need to go back China to obtain a re-entry visa for US. I am looking for cheap airfare for this multi-stop trip and found this great site with a lot of helpful information. As far as now, the best I can get will be flying via JAL with the following itinerary for $962 including tax/fee through a local travel agent.
Oct.26 JFK-NRT
Nov.2 NRT-PVG (Shanghai)
Nov.20 PVG-NRT
Nov.20 NRT-JFK

The better choice will be flying to KIX, though the air fare will be about $200-$300 more and my local agent can only get the HND-KIX not the NRT-ITM. Another concern is the time issue for traveling from NRT to HND to catch the plane. Plus I have two big luggage with me which will be a big problem. So currently I have some plans:

1) But this $962 ticket through the agent and call JAL to purchase the $200 two sector oneworld Yokoso/Visit Japan Fare for NRT-ITM. Is this option feasible? Or I have to buy the whole ticket through JAL directly?
http://www.jal.co.jp/yokosojapan/

2) Buy the 7-day JR Pass in advance in US and take the bullet train from Tokyo to Kyoto, and spend $100 for the baggage storage at NRT airport. The only concern is about the Japan visa, I heard the application for temp visitor visa is a whole of trouble for Chinese in US without US re-entry stamp. So I am going to apply for the 15-day transit visa, will that account for "sight seeing" as well? I am little bit confused by the wording here:
http://www.jtbusa.com/enhome/jrpass.asp

Any advice about this trip will be appreciated, thanks a lot for reading!

Even if you land at KIX or ITM you have to handle your luggage. It is 100 km around to Kyoto. So why not fly in NRT, send the two suitcases from NRT to Kyoto accommodation ( around Yen 2000 per piece one way ) and then by Narita Express and shinkansen to Kyoto. Because of the airport change NRT/HND you will need same time for flying or by shinkansen.
Regarding proper visa check consulate.

My gut feeling is that you will not have a big problem as long as you have an exit ticket. But it is a good idea to check Embassy/Consulate.
http://www.us.emb-japan.go.jp/english/html/index.htm

The transit visa issued by our local Japan consulate is a little confusing. The visa is for a citizen of Thailand.

We fly from the US to Thailand on May 19/20. We transit through Narita on the 20th, but we don't leave the airport. We come back to Tokyo on June 1 for a three night stay.

We got a transit visa with an expiry of May 30, for a stay of 15 days.

Does anyone review the passport/visa for travelers who only transit in Japan? I think it is strange that it expires two days before our trip into Tokyo.

Thanks!