Advice on 2nd time: Alps, Nagasaki, Okinawa

This is our second trip to Japan. Our first trip was in November and we went to Tokyo, Takayama, Kanazawa, Kyoto (4 days), Nara, Koyasan, Himeji, Hiroshima and Miyajima. We thoroughly enjoyed it.

This time we want to start with Tokyo again, have 3-3.5 weeks and thinking of arriving mid october (flight is not booked yet, so shift is possible)

Nagasaki is maybe a bit of a stretch, but we are interested in this, also because of our Dutch background. Also, we like traveling on the Shinkansen, so a long travel day is not a problem.

Would like to hear your ideas on this itinerary and also if you have any ideas for day 11-13. Or should we instead add some days somewhere to the existing destinations?

Day 1 -5: Tokyo (arrival at day 1, so 4 full days)
Day 6: Travel to Matsumoto (2.5/3 hours), explore matsumoto (+ possibly wasabi farm)
Day 7: day trip to Kamikochi (or better to overnight there?)
Day 8: Explore Nakasendo way (Narai + walk?) (stay in Tsumago?)
Day 9: Explore Nakasendo way (Magome to Tsumago) (stay in Tsumago)
Day 10: Travel to Nagoya, visit Toyota commemorative museum,...

Day 11-13: open, include travel time/day to Kyushu.
E.g. Fukuoka? Beppu? Or some other idea?

Day 14: Travel to Huistenbosch, visit park, overnight in robot hotel.
Day 15-16: Nagasaki
Day 17: Fly to Naha (from Nagasaki)
Day 18: Naha (visit aquarium + some other highlights)
Day 19: Fly (early) to Ishigaki
Day 20-22 Explore Ishigaki (incl Taketomi, Iriomote)
Day 23: Fly from Ishigaki to Osaka or Tokyo (Evening)
Dag 24: Fly home (Early morning)

You are Dutch, right? What about some light cycling on the two open days?
Eg go to Okayama (on your way to Nagasaki anyway) and stay there two nights. One day you can cycle in the Kibi plain ( http://bicycletraveljapan.blogspot.nl/2017/11/day-45-kibi-plain-and-ku... )
and if you have time the next day you can go to Bitchu Takahashi and the garden in Okayama or to Inujima art project.

Just one idea to fill those two days. There are for sure hundreds of alternatives.

Enjoy your trip to Japan!

It's been a while, but thank you for your response!

We indeed like cycling, so it is a good idea. We are now even thinking of adding a day to the schedule and then do the Shimanimi Kaido in 2 days. Any experience with that? We will be there begin november, so hopefully the weather is good.

We cycled last time in Hida Furukawa (Gifu), with a guide (Satoyama experience) and we really ejoyed that.

Other things in our itinerary which I still doubt about
- Kamikochi: is this doable as a day trip is an overnight stay recommended (and worth the price)
- Okinawa: am now thinking of adding a night in Iriomote, but still do not have agood feel whether this is a good itinerary.

Feedback appreciated!