Rail pass yes or no

Hello,
We have finalized our itinerary in Japan.
5 of us are travelling from Tokyo to Kyoto on the 9th of April (early morning if possible) where we shall be staying two nights,
On Friday April 11 we are continuing our journey to Osaka airport where we shall stay the night.
On Saturday morning two of my sons are flying to Okinawa.
3 of us are spending one additional night in Osaka and are travelling to Kanazawa on the April 13. we shall be staying three nights and travel to Nagano on April 16 . there we shall be staying two nights and will travel from Nagano to Tokyo on April 18.
One of my sons will need an additional train ticket from Osaka to Tokyo on Saturday. April 19.

Could you advise us please how we are going to book our rail passes.

Stefanie