How to plan our itinerary in Japan
 

Hi, my family plan to visit Japan in November for 8 days. This is our first time travelling to Japan. Plan to visit the places below . need advise on the travel train pass and if can, how to plan our itinerary. Tqvm

1. Mt fuji

2. Disneyland

3. Tokyo tower

4. Tokyo skytree

5. Shinjuku

6. Shibuya

7. Ginza

8. Asasuka

9. Harajuku

10. Tokyo station, marunouchi

11. Tsukiji

12. Imperial palace

Almost every place you have listed is in Tokyo - only Mt Fuji is not in Tokyo, and it is nearby. So a rail pass makes no sense at all. You will likely want to buy stored value cards for the subway system. These can be purchased at any station and you can add money to them at any station.

The best info on Japan on the web is at www.japan-guide.com

For Mt. Fuji, do you want to go to the mountain, e.g., Five Lakes region or do you want beautiful views of Fuji? If you are looking for the views, you might want to go to Hakone. Also, since you are planning all of your time in Tokyo, you might appreciate a couple of nights away from the big city.

As noted above you are spending nearly all your time in Tokyo, which is kind of a waste. I suggest you spend about 3 days to see Tokyo, a day for Disneyland if you really want to see it (avoid the weekends if possible), and the rest of your time for some great day trips outside the city.
For transport within the city, look at a 3 day subway pass, which is easy to recoup the costs and save some money.
http://www.tokyometro.jp/en/ticket/v...dex.html#anc03

For Fuji, you won't be climbing it, and the best views are from either Hakone or the Fuji 5 Lakes area. I think the Hakone loop course would serve you pretty well. You can use a Tokyo Wide Pass to get part of the way there as well as for other day trips.
http://www.japan-guide.com/e/e2361_06.html
For going into Hakone, look into a Hakone Free Pass used from Odawara Stn.
http://www.odakyu.jp/english/deels/freepass/hakone/
http://www.japan-guide.com/e/e5210.html

For other day trips, there is Nikko, Kamakura, Kusatsu, Izu, etc.

Also if you are already going to see the Sky Tree, going to the Tokyo Tower is really redundant and a waste of money. If you really love city views, there are many free alternatives.
http://supermerlion.com/10-free-tokyo-city-views/

You are also giving districts you want to see, not specific places. You'll need to narrow down your plans more. Have a look at some specific places to see on:
http://www.gotokyo.org/en/index.html
http://www.ar.jal.com/world/en/guide...o/see/akasaka/
http://www.japan-guide.com/e/e2164.html

Mt Fuji could be seen even from Tokyo, but the odds is much higher if you get closer. In this sense, Kawaguchiko in Fujigoko area would be better than Hakone. Hakone is a more attractive resort, though. You could spend a night there to enjoy a slow pace travel, or just pick the best weather day while you are in Tokyo.

http://www.japan-guide.com/e/e2172.html
http://www.japan-guide.com/e/e6933.html
http://www.japan-guide.com/e/e6905.html
http://bus-en.fujikyu.co.jp/highway/

Tokyo Disney Resort is a set of Tokyo Disneyland and Tokyo DisneySea. Both would need at least one day to go around.

http://www.tokyodisneyresort.jp/en/

The rest could be divided into roughly four regions. If you filled up four weekdays for the above, you could spend each for a day. Harajuku would be better in the weekend. Tokyo Tower would be better for a night view, while Tokyo SkyTree in the day, may be in the early morning. Of course, you could devote two days for a area, especially for Tokyo and Ginza.

Tsukiji/Tokyo station, Marunouchi/Imperial Palace/Ginza/Tokyo Tower
Tokyo SkyTree/Asakusa
Shinjuku
Harajuku/Shibuya

I think an IC card would be the most easy solution. There is almost no restrictions that could not be avoidable with any passes. Once you have got to each area above, you could walk around. Thus, only tickets to and from the hotel would be necessary. For sightseeing, I recommend surface transportation rather than undergrounds.

http://www.japan-guide.com/e/e2359_003.html
http://www.kotsu.metro.tokyo.jp/eng/...us_ticket.html
http://www.kotsu.metro.tokyo.jp/eng/.../bus_ride.html
https://www.tokyo-park.or.jp/waterbu...f/sanpo_en.pdf
http://www.jreast.co.jp/e/pass/tokunai_pass.html

Do utilize Google Maps to select a method by comparing time and price. You could specify your hotel name between slashes in an example below.

https://www.google.com/maps/dir/toky...n/tokyo+tower/

Are the numbers in your original post the days/ nights or simply the order of interest in the attractions listed?