Hello there,
Looks like you are planning a very nice family trip!
Unfortunately you won't be able to Tokyo on the day of your arrive. The journey is about 250 minutes, the last train you could take from Kansai Airport to Tokyo leaves at 19.15, this because trains don't ride past midnight. So I would recommend that you stay your first night in Osaka and take an early train to Tokyo.
The ticket office at Kansai Airport is open until 23.00 so you should have no problem to exchange your passes on the day of arrival. You could book a hotel around the airport or in Osaka itself. I have found that Best Western Hotel is affordable and very well suited for transit trips stays. http://bit.ly/12bD5Tt
Here is an example of what your journey from Kansai Airport to Fifty's Family Resort in Tokyo would look like. http://bit.ly/W9EYMa
I think that Fifty's Family Resort is very well suited for your stay in Tokyo because it is very close to Disney Land, while its not in the city centre you can use your JRPass to get there in 15-20minutes. While in Tokyo I would recommend that you visit the Sensō-ji Temple and Kaminarimon in Asakusa. http://en.wikipedia.org/wiki/Sens%C5%8D-ji
If you would like to see and shop Japanese fashion, then I would recommend that you pay Harajuku a visit, you can combine this with more luxurious shopping at Omotesando http://en.wikipedia.org/wiki/Omotesando and a visit to the Meiji Jingū shrine http://en.wikipedia.org/wiki/Meiji_Shrine, both are closely located to each other.
For more shopping I would recommend Shibuya (Youth culture) Akihabara (Gadgets, Electronics and everything Anime) and Shinjuku (very busy and a bit of everything). Tokyo is really big, so if there is anything in particular you are looking for let me know and I can give you some more detailed recommendations! I would also recommend a visit to Imperial Palace in the middle of Tokyo, it has a very beautiful park.
When you get back to Osaka and still want to see more temples, than I would recommend a day trip visit with your JRPass to Kyoto, which is only about a 30 minute ride. Here you could visit some of the famous temples such as the Golden Pavilion http://en.wikipedia.org/wiki/Kinkaku-ji and Kiyomizu-dera http://en.wikipedia.org/wiki/Kiyomizu-dera. Also if you have time, then Osaka Castle is surely worth a visit. http://www.osakacastle.net/english/
Again I think Fifty's Family Resort Osaka will be suitable for your stay, on its website it states that it is only a 10minute bus ride to Osaka station and from there you could use your JRPass to visit places such as Kyoto and Universal Studio's.
Here's a map that can be very useful for planning your your travel around Osaka. http://bit.ly/UdNPe0
For shopping start either at Namba or Umeda and walk your way to Shinsaibashi, which is the centre for shopping in Osaka http://bit.ly/UoMJM8 . On your last day consider Rinku Town, this is one of the biggest shopping malls I have ever seen and is closely located to Kansai Airport.
Buses that are operated by JR are mostly covered by the Pass but many buses are operated by other companies. We have a nice article about your JRPass and buses: http://www.jrpass.com/blogs/how-to-use-the-city-bus
Hope this helps!
-Daniel
