[Flights, accommodations and the order of places]
Assuming that you can rebook your flights and accommodations with no or little additional cost, I suppose it may be better to fly into Narita Airport [NRT] or Haneda Airport [HND], tour Tokyo, travel to Kyoto, tour Kyoto and fly out from Kansai Airport [KIX].
November 24 of 2014 will be a substitute holiday because the previous day November 23 will be a national holiday and a Sunday. So, the weekend from November 22 will be practically expanded to be 3 days until November 24.
During these 3 days, popular tourist spots may be crowded, especially some in Kyoto City if they are still in the autumn foliage season. Also, Tokyo Skytree and Tokyo Disney Parks may well get many visitors including kids.
Anyway, regardless of whether you tour Tokyo earlier or later, I suppose November 25 (Tuesday), which will be a normal weekday, may be better for you to visit Tokyo Disney Resort in terms of possible crowdedness.
Also, staying overnight in TDR is worth considering.
A guest of any of the three Disney Hotels + the six Tokyo Disney Resort Official Hotels can purchase a Tokyo Disney Park ticket in the hotel, and can be guaranteed admission to the Disney Park on the specified day if entry is restricted due to crowdedness outside the Park.
http://www.tokyodisneyresort.jp/en/about/rh/index.html[Tokyo trips and traveling to NRT]
Could you clarify what you will visit in Shinjuku, Shibuya, Ginza and Asakusa areas and which station is good for your Asakusa hotel?
Many routes are possible, and it is difficult to recommend specific routes without knowing locations of your starting point and destinations.
[JR and Sagano Scenic Railway tickets]
we arrive Kansai airport at 9am. From Kyoto to Tokyo, we plan to take Shinkansen, ticket can be purchased at Kyoto station or can we buy at Kansai airport? You can purchase your JR tickets, ICOCA Cards and Sagano Scenic Railway (Romantic train) tickets for this journey all in the JR Ticket Office in Kansai-airport Station.
You are highly likely to become free to travel by the noon, so you can have enough time to get them.
The 5-year-old kid, when he/she is accompanied by an adult and does not use a reservation-requiring facility, can travel by rail basically free of fees.
When he/she has a reserved seat, child-rate fees (= basic fare and additional charge) are required.
[Form KIX to Uzumasa]
Which train company should we use to travel from Osaka to Kyoto? The company is JR-West [West Japan Railway Company], which is one of the six JR regional passenger railway companies.
JR Ltd. Express "Haruka" trains are connecting Kansai-airport Station and Kyoto Station in roughly 1 and a half hour per way.
JR "Haruka" trains from KIX use Track 30 or Track 0 of Kyoto Station.
You may need to wait for your second train for about 20 minutes in Kyoto Station.
You can take a JR Local train on Sagano Line from Kyoto (departing at nearby Track 31, 32 or 33) to Uzumasa for about 15 minutes. (Faster trains skip Uzumasa Station.)
Is it correct to say we should buy the Haruka & ICOCA to travel from Kannai to Kyoto station? There seems to be no child-rate edition of the ICOCA & Haruka packages.
I suppose the 10-year-old kid and the 8-year-old kid can choose the packages just as adults do. (They can return the adult-rate ICOCA Cards in Uzumasa Station, paying 220 yen per card as a handling fee.)
If they cannot choose the packages, the JR cost to get to Uzumasa is estimated at 1520 yen per child, which consists of 940 yen + 100 yen as child-rate basic fares covered by a Child Suica Card and 480 yen as a child-rate Ltd. Express charge (without seat reservation) paid separately in advance.
A Child ICOCA Card is issued by JR-West in its office, with personal data of the holder (such as the date of birth) registered.
The JR cost for the four adults to get to Uzumasa is estimated at 1230 yen per adult, which consists of 1030 yen on the ticket in the package (without seat reservation) + 200 yen as a basic fare covered by the ICOCA Card.
The ticket in the ICOCA & Haruka package is not valid on JR Sagano Line.
Please note that each of you will exit JR once and enter JR again in Kyoto Station. Central Gate is near the platforms for your trains.
For your information: A studio park managed by a major Japanese film company's affiliate is located near Uzumasa Station.
http://www.japan-guide.com/e/e3934.html[Kyoto and Osaka trips]
Which places in Osaka City will you visit? Only Dotonbori food-and-drink area?
To visit Kiyomizudera Temple, Gion district and (Fushimi) Inari Shrine in one day, you can use Kyoto City buses.
A Kyoto City Bus - Kyoto Bus One-day Pass can pay off in two or more rides inside the fixed-fare zone, which includes the bus stops for these places.
The pass for an adult (roughly over 12) is sold at 500 yen. The pass for a child (roughly 6 to12) is sold at 250 yen.
You can purchase these passes in the bus information center near Central Gate of Kyoto Station.
You can take one JR train on Sagano Line for a few minutes (in the opposite direction of Kyoto Station) from Uzumasa Station to Saga-Arashiyama Station, which is near Torokko Saga Station of Sagano Scenic Railway.
http://www.sagano-kanko.co.jp/brochure/english.pdfAn ICOCA Card / a Child ICOCA Card can be used to travel between Uzumasa and Saga-Arashiyama. The one-way fare is 140 yen / 70 yen.
IC transportation cards such as ICOCA Cards are not accepted on Kyoto City Bus lines, Kyoto Bus lines or Sagano Scenic Railway line.
A Kansai Thru Pass is a non-JR transpiration pass. In your current itinerary, probably you will not have chances to use non-JR lines enough for this pass to pay off.