Need help with Japan 12 day visit

We are a family of 5 (9,7, and 5 year old)to travel to Japan in October. We arrive at 8pm into Tokyo on 4/10 and all the limousine buses won't be running. I am not sure what the best way in terms of train passes to get to Maihama Station as we will be staying in Tokyo Bay. I am totally confused with JR passes, Suica pass, 2 day passes, Tokyo Metro tickets etc. and i have the forums and websites! i would love any suggestions to my itinerary and recommendations on what to buy. This is the plan
4/10 Arrive in Narita
5/10 Tokyo Sightseeing (staying in Tokyo Bay)
6/10 Disneyland
7/10 Disney at Sea
8/10 Tokyo Sightseeing
9/10 Head to Kyoto
10/10 Himeji Castle
11/10 Hiroshima +/- Miyajima
12/10 Kyoto/Nara?
13/10 Head back to Tokyo
16/10 Leave from Narita 9pm flight

Should i base myself in Kyoto or Osaka? Also with the travelling i think the 7day JR pass will not cover any travel for Narita-Tokyo, so what is the best tickets for me to get? Also are there any places that are a must-see i have left out??

If you miss the direct buses, it is surprisingly complicated to travel from Narita Airport to Disneyland. For simplicity, I would be taking the Narita Express from the airport to Tokyo Station and then the Keiyo Line to Maihama, but note that the platform of the Narita Express is about a ten minute walk away from the platforms of the Keiyo Line.

As for your itinerary, I think you should be spending a little bit more time in Kyoto itself. The city has a lot to see.

Also with the travelling i think the 7day JR pass will not cover any travel for Narita-Tokyo, so what is the best tickets for me to get?

I recommend to purchase the NEX&Suica package, use the NEX (Narita Express) on the first day (as mentioned above) and use the Suica card on train travel in Tokyo before you activate the Japan Rail Pass.

Also are there any places that are a must-see i have left out?

Certainly! But it can't be helped. You cannot see all must-see places in just 12 days. I think your itinerary is already very fast-paced.

Thank yous Uji for your input. So are you saying that i get N'ex Suica for Day 1, and on last day 17/10 i get a limousine bus to go back to Narita as my 7 day JR pass will have expired as i will activate it on 9/10. And to confirm best to stay in Kyoto, not Osaka? As we are going from Fri-Tues, will there still be lots to do in Kyoto? i know the Kyoto Palace is closed so i had to book tour on 13/10 my last day in Kyoto.

So are you saying that i get N'ex Suica for Day 1, and on last day 17/10 i get a limousine bus to go back to Narita

I did not comment on your trip back to the airport. I recommend to make a choice of transportation based on the location of your hotel.

And to confirm best to stay in Kyoto, not Osaka?

Since you do not plan to see Osaka, I recommend to stay in Kyoto. Or, as mentioned before, to also stay a night in Hiroshima or Miyajima. I recommend staying on Miyajima, in particular.

For example:
09/10 via Himeji to Miyajima
10/10 Miyajima/Hiroshima and then to Kyoto
11/10 Kyoto
12/10 Kyoto/Nara
13/10 Kyoto and back to Tokyo

As we are going from Fri-Tues, will there still be lots to do in Kyoto?

Yes. Nothing (except the imperial buildings) is closed on weekends. But it will be very busy. How about making your trip to Western Japan after the long weekend (from 11/10)? Then, your rail pass would also cover the train journey back to the airport.

Thanks Uji. Now i am considering to stay in Mirayima. I noted that you just i go there via Himeji, but with timetabling how will that work- as i am leaving from Disneyland Tokyo and the train down to Himeji is 4.5hours approx. Then how long would i stay at Himeji as if i was to travel then down to Mirayima that is another 2 hours so we would get in quite late. Would we miss seeing the shrines arriving so late? The whole point is to see the shrines with water. Maybe it is too ambitious??

The average traveler spends about 3-4 hours in Himeji. Whether it is feasible depends on how early in the morning you leave Tokyo and on your preferred pace of travel and strength.

For example, if you leave your hotel around 7am, you can get to Himeji Castle by noon, stay 3 hours in the city and arrive in Miyajima around 5pm. Sunset is around 17:45.

It is a busy day, but if you do not mind a fast pace, it can be done.

Miyajima can be seen that evening and next morning.

Whether you can see the shrine with water depends on the tides of the day. You can look them up here:
http://tbone.biol.sc.edu/tide/tideshow.cgi?site=Itukusi...

On October 10/11, the timing is not favorable. High tide takes place at 13:58 (before your arrival) on October 10 and 1:07 (while you will be probably sleeping) and 15:13 (after your departure) on October 11.

Yes i had checked that website and the high tide times are awkward to my scheduling.8( However how fast does the water recede to mud flats from 2pm if we get there by say 3:30pm. I think we will give Himeji a miss on the way down so to not miss Miyajima and its surroundings. How long should i spend in Hiroshima to see the"key"sites? Perhaps i could head to Kyoto via Himeji instead- what do you think?

how fast does the water recede to mud flats from 2pm if we get there by say 3:30pm.

I think for at least +/- 2 hours, the shrine will not be in water. At 3:30pm, you will most likely still see the soil instead of water.

How long should i spend in Hiroshima to see the "key"sites?

I rcommend half a day for the peace park. Do you plan to see anything else?

Perhaps i could head to Kyoto via Himeji instead- what do you think?

Yes, that is another option. Also, beware of luggage issues. If you travel light, it should be no problem, but if you have some big pieces of luggage, it might be better, for example, to use a delivery service to send your big luggage from Tokyo directly to Kyoto and do the Miyajima/Hiroshima side trip with only some smaller bags. Otherwise, you will have to look after your luggage all the time along the way in Miyajima and Hiroshima and possibly Himeji.

i thought there might be luggage lockers at train station or rail-on service which i read on the forum?? is there such in Hiroshima and Himeji? Are the train station close to the tourist attractions?

Yes, there are lockers at all major and many minor stations, but it can still be a hassle to find vacant ones that fit large luggage.