Three weeks in Japan

I am trying to plan for three weeks in Japan in July / August 2018. I will be in Taiwan for a week before this. I was thinking Taiwan to Okinawa ( eight days split between Naha and Ishigaki island ). Fly to Osaka 4 days, then Kyoto 4 days , Kanazawa, Shirakawago, Takayama, mabe 2 days each or just go to 2 places but which ones? Then Tokyo for 4 to 6 days, does this itinerary make sense ,and what is the best way to travel 7 day pass or longer, I know this is more than three weeks so I need to trim it a bit or I can go for a little longer than three weeks if req.