Help with 14 days Honshuu interary

Hi there
Me and my boyfriend are arriving in Tokyo on the 15th of September and flying out from Tokyo on the 29th.
We need help with planning the interary.
I would like to spend 2-3 days in Tokyo, 2 days in Osaka, 2-3 Kyoto - and see the bamboo forest. Visit Kanazawa and Shirakawa go. But I would like to also see more of rural Japan and rice paddies if possible. Could you please recommend places that we can see with Jrpass or if the travel is not included which trains should we take. I would like to also see Mt Fuji - even from train.

I would appreaciate your help. Thank you in advance!