Rail Pass Advice

Hi there,

We have finalised our itinerary for Japan but are unsure what to do about the rail pass. Due to a lack of hotel availability, our itinerary isn't exactly what we wanted but we are quite happy with it.

1 night in Kobe - explore Himeji the next day

2 nights in Kyoto - explore kyoto both days

2 nights in Osaka - explore osaka and possible day trip to nara

2 nights in Hiroshima - one day go to Miyajima

3 nights in Tokyo

2 nights in Kusatsu Onsen

2 nights in Tokyo

Given the plan, what is the best solution for rail passes? I assume we will need a JR pass but ideally I only want to buy the 7 day one and activate it for the long trips. I have found a number of localised rail passes that include the subway and bus.

If anyone has any idea on the best way to do this it would be much appreciated.