Hi there!
There's certainly a place for a JR Pass in your itinerary. Going to Hiroshima or Tokyo will allow for some good savings, especially since Shinkansen travel is included.
Being able to spend 2 months in Japan is absolutely great but finding the right pass may be a bit of a challenge because of this. JR Passes are available in 3 flavors, 7 Days, 14 Days and 21 days. Since you want to take your time you could for instance consider a two week pass and use it to cover most of your Shinkansen travel. An other option would be to go for 2 separate passes such as 2 times a 7 day JR Pass and use them at different times.
Either way the JR Pass offers a lot of flexibility.
I hope this helps!
Daniel