5 days in Tokyo, 3 days with JR Kanto Pass

I will travel to Japan from 29 Aug to 2 Sept 2012. Plan to buy JR Kanto Pass (3 days) to travel to Nagano and Kawaguchiko area. Another 2 days will sightseeing around Tokyo city including half day trip to Disneyland.
My question is:
1. Will be in Haneda airport early morning. I plan to visit Tsukiji by boarding the earlier train . Should I cancel my Tsukiji and wait at Haneda airport till the JR counter open at 11am, then I can buy JR Kanto Pass and may used it immediately for airport transfer?
2. Do I need to book in advance for Shinkasen from Tokyo to Nagano? I had booked the accommodation in Yudanaka, afraid if I couldn�ft get the seat to Nagano.

3. In Tokyo, which part of the city is convenient to stay? In my mind is Shinagawa, Ueno or Shinjuku?
4. Initially I plan to go for a half day Disneyland trip with Starlight Passport on weekdays to avoid the crowd. The Disneyland website schedule shown Starlight Passport not available from 29~31 Aug 2012. Only available is Natsu 5 Passport . What is Natsu 5 Passport? What is the price?

5. Is Art Museum, Railway Museum and Mitsubishi technology Musem in Yokohama open in Saturday and Sunday? What is the opening time?
Following is my plan itinerary, will be revised subject to suggestion on above question. Appreciate any suggestion/feedback:
1st day : Early morning, from Haneda Airport travel to Tsukiji . Then proceed to Nagano, put a night in Yudanaka.
2nd day : from Yudanaka travel to kawaguchiko. Put a night in Kawaguchiko.
3rd day : from kawaguchiko to Atami then back to Tokyo
(above 3 days using JR Kanto Pass)
4th day : Morning-Tokyo sightseeing. Afternoon visit Disneyland
5th day : Visit Omiya Railway Musem, Yokohama-Mitsubishi technology museum, Tokyo sight seeing.

I will travel to Japan from 29 Aug to 2 Sept 2012. Plan to buy JR Kanto Pass (3 days) to travel to Nagano and Kawaguchiko area. Another 2 days will sightseeing around Tokyo city including half day trip to Disneyland.

Sounds good to me.

My question is:
1. Will be in Haneda airport early morning. I plan to visit Tsukiji by boarding the earlier train . Should I cancel my Tsukiji and wait at Haneda airport till the JR counter open at 11am, then I can buy JR Kanto Pass and may used it immediately for airport transfer?

No, that would be a huge waste of time. I would just pay the individual fare to Tsukijishijo station which will be somewhere around 550-640 yen. Note that you can't access Tsukijishijo with a JR Kanto Pass anyway.

If you want to buy the JR Kanto Pass after Tsukiji you can purchase it at Tokyo Station (from 7:30am), or a few of the other stations.

You can use Hyperdia for train timetable planning:-
http://www.hyperdia.com

2. Do I need to book in advance for Shinkasen from Tokyo to Nagano? I had booked the accommodation in Yudanaka, afraid if I couldn�ft get the seat to Nagano.

There are 30+ Shinkansen per day from Tokyo to Nagano, and plenty of other options for getting there. I'm sure you will have no problems getting a seat booking on the same day of travel. Worst case you can try the non-reserved cars, or you can stand.

3. In Tokyo, which part of the city is convenient to stay?

A good explanation:-
http://www.japan-guide.com/hotels/tokyo.html

In my mind is Shinagawa, Ueno or Shinjuku?

Yes. I tend to prefer Shinjuku but have also stayed in a few other areas including Ueno.

4. Initially I plan to go for a half day Disneyland trip with Starlight Passport on weekdays to avoid the crowd. The Disneyland website schedule shown Starlight Passport not available from 29~31 Aug 2012. Only available is Natsu 5 Passport . What is Natsu 5 Passport? What is the price?

Natsu 5 lets you enter at 5pm for 3300yen. Same price as Starlight but one hour earlier.

5. Is Art Museum, Railway Museum and Mitsubishi technology Musem in Yokohama open in Saturday and Sunday? What is the opening time?

Omiya Railway = Yes, 10am
Art = Yes, 10am
Mitsubishi = Yes, 10am

Following is my plan itinerary, will be revised subject to suggestion on above question. Appreciate any suggestion/feedback:


Looks busy and a fast pace but fine if you like that.

Enjoy your trip!

Thank you GC3 feedback.

Disneyland ticket:
I will go Disneyland on the first day on 29 Aug. The ticket is open for sales 1 hour prior to the opening. If i reach there around noon, is it possible to get the ticket? Alternatively can i book the ticket online?

As we plan to visit Art Museum in Ueno, so think of staying in Ueno. What is the traveling time to Disneyland.

Tsukiji fish market:
Read that the Tsukiji Market tours only allow 120 visitor daily.Visitors have to check in at 5am.
Can i arrive there on time by public transport?
Some article wrote that the tsukiji market close on certain Wednesday. on 29 Aug (Wednesday)?

Thank you GC3 feedback.

No worries.

Disneyland ticket:
I will go Disneyland on the first day on 29 Aug. The ticket is open for sales 1 hour prior to the opening. If i reach there around noon, is it possible to get the ticket? Alternatively can i book the ticket online?

It is all explained here:-
http://www.japan-guide.com/e/e3016_tickets.html

As we plan to visit Art Museum in Ueno, so think of staying in Ueno. What is the traveling time to Disneyland.

Go from Ueno to Tokyo station and follow this:-
http://www.japan-guide.com/e/e3016_access.html

Tsukiji fish market:
Read that the Tsukiji Market tours only allow 120 visitor daily.Visitors have to check in at 5am.
Can i arrive there on time by public transport?

It is explained here:-
http://www.japan-guide.com/e/e3021.html

No, taxi will be best. 2500-3500yen I guess. I would try and arrive at 4:30am at the latest.

Some article wrote that the tsukiji market close on certain Wednesday. on 29 Aug (Wednesday)?

http://www.tsukiji-market.or.jp/etc/calendar/2012.html

Open on the 29th.