13 days Itinerary with 7 days JR PAss

Hi Dear,

I am going to Japan for the first time with my Fiance for our Pre Wedding shoot.
Will reach Haneda on 23 Nov - 06:15 am and leaving on 05 Dec - 22:55.

My photo will be on 29 Nov at Kyoto (on 29 night will travel to Tokyo by Bullet Train) and 30 Nov at Tokyo.

Can anyone suggest how should i plan for my itinerary?

Planning to get 7 days JR Pass only and wish to go to below:-

Tokyo
Kyoto
Osaka
Nara (if a nice place to visit)
Miyajima day tour
Japanese Alps: Takayama, Shirakawa-go and Kanazawa
Mt Fuji (Should i go with tour?)
Disney Sea
and other popular museum

At Tokyo can i just buy 3 days Metro Pass?

On first day when i reach, should i go Osaka/ Kyoto directly? or stay at Tokyo fo 1 or 2 nights?

Please help me. Thanks!