First time Japan trip

Hi, we are in our 60 and used to travelling but feeling rather overwhelmed .
We will have 21 days in Japan and want to go to Tokyo, Kyoto, Hakkone- with all side trips - and Naoshima Island as well as going to Hiroshima ,Nagoya and passing thro Shirawago.
So far we have booked ;
Tokyo 3 nights
Hakkone 3 nights
Kyoto- not yet booked ? 5 nights
this is where we run into problems


we want to go to Naoshima island but are unsure which route and stop over to use.
We also want to see something of Matsuyama and Hiroshima Takayama , Shirakawa go Kanazawa before returning to Tokyo for ou flight .
Where does Osaka or Okinawa fit in ?
We would rather not rush so might prefer 2 night in some places .
Your advice would be gratefully appreciated.
There is so much we would like to see but so little time
many thanks

Are you flying in and out of Tokyo? If so you could plan a circular route,
What do you want to experience on this trip? This would help us with our suggestions.
Offhand, I would stay two nights max at Hakone.

Okinawa should not be in your itinerary. Flying there takes 3 hours from Tokyo or 1.5hrs from Fukuoka and it's way out of your way.