Should we get the JR Pass?

Hi there,

Yes, the JR Pass will cover nearly all travel here but you may also need to use some additional transport.

For instance, you can use the train to Ōkunoshima but the last part on the ferry is not included.

The same applies for Fuji, details can be found here:
http://www.jrpass.com/blogs/itinerary-tip-mt-fuji

I can say for sure when I have your full itinerary but as far as I can see you will be covering a good amount and a 7 day JR Pass would definitely help you make savings, likely a 14 day JR Pass as well.

You can use the JR Pass Fare Calculator to find an approximate ticket cost of a single route or even your full itinerary.

Hope this helps,
Daniel