Hi there,

It's a bit of research to find these routes but once you have them written down, it will be much easier to understand.

How to get to Shirakawa-go:

Here is how to visit Shirakawago using the JR Pass.

How to access Naoshima:

You can access Naoshima by ferry from either Uno or Takamatsu. Going via Uno is by far the faster route while going via Takamatsu is more Scenic. Using the JR Pass you can take the Shinkansen to Okayama station and then a local train to Uno station. From there it is about 5min walk to the ferry terminal to Naoshima (the ferry is not covered by the JR Pass but the fare is low). Alternatively, you can also take the train from Okayama to Takamatsu going over the Great Seto-Ohashi bridge. This is a very scenic ride when the weather is good and you can have a panoramic view over the Shikoku islands. From Takamatsu station it is 5min walk to the Ferry.

Hope this helps,
Daniel

Thank you for your reply. Do you think we should get a 14 day pass? Should we buy a 7 day and just pay the return out of pocket? Will the JR cover the day trips? Also, we decided we will skip Shirakawago.
So this is what we have:

June 5- Day 1-Arrive Tokyo
Day 2-Full day Tokyo Day 3- Nikko day trip June 8- Day 4- Travel to Osaka- Activate JR
Day 5- Osaka Full Day Day 6 -Osaka Full Day June 11-Day 7- Hiroshima/Miyajima Island travel to Okayama, stay overnight
June 12- Day 8-Naoshima, overnight Okayama
June 13- Day 9- Kyoto
Day 10- Nara Day Trip Day 11- Kyoto June 16- Day 12-Kyoto/Travel to Tokyo
Day 13- Tokyo Full day Day 14- Tokyo Full day June 19- Day 15 - Tokyo to Airport

Any suggestions?
Thanks in advance!