Travel questions

1. Am planning 15 day holiday 2nd half September with 4 nights Tokyo, 2 Nagoya, 2 Takayama, 3 Kyoto and 3 Osaka flying into/out Narita. Is my best option for internal travel to get 14 day JR pass plus Sucai/NEX package?
2. Himeji looks like it may be a no-go late September. Any alternatives?
3. Is Kamakura or Hakone better for a day trip from Tokyo?
4.Do museums etc. usually close on PHs?
5. How easy is it to prebook intercity train journeys especially for PHs? How far in advance can I book?
6. Do I need to prebook the bus to/from Shirakawago from Takayama?
Many thanks

1. It seems that 14 day rail pass works for your itinerary

2. If you are going this Sept., chances are you can still see Himeji Castle before it is completely covered in March 2010 for its restoration.
http://www.jnto.go.jp/eng/location/regional/hyogo/himej...

3. As a daytrip, Kamakura is more suitable. Hakone deserves 1 night stay.

4. Different museums may have different closing dates in the week, but during public holidays usually most are opened.

5. You can reserve your train seats once you activate your rail pass.

6. Since you are staying overnight in Takayama, you can book the Shirakawa-go bus the night before departure. We did, and on the day of travel, there were only about 10 people onboard the bus.