It looks to me to be a pretty sensible itinerary. There are still a number of good places in Kyushu to see, but it takes a lot more time.
Doing the Shimanami Kaido can be a very rewarding experience, although a pretty good workout. You'd also have a chance to see Kosanji, which is one of the wildest ornate temples in Japan - some call it a "Buddhist Disneyland".
https://www.youtube.com/watch?v=97Q5EjEOXI8There is a daily flight from Fukuoka to Yakushima by JAL, but the fare is pretty high for the one hour flight (nearly 25,000 yen one way). As I recall, it is under JAC so it is not eligible for its Yokoso discount fare. The trouble you're having may be due to being unable to issue tickets for it outside of Japan - only an agency or JAL can do it in Japan. There are more flights to Yakushima out of Kagoshima.
It's good you schedule a little down time after your long flight from London - most likely you'll arrive half dead. Fukuoka has some good places to see though. There are several good parks to see, and good views over the city from the Fukuoka Tower, Minami Park tower, and Aburayama. Plus good food, a lively night district, and more.
http://www.thejapanfaq.com/fukpic.htmlhttps://www.youtube.com/playlist?list=PL7LcPcmoSg-j4RLa6iC7ayvBAbOn8-0...One of the best temples you'll ever see in Japan is just 25 minutes or so from Hakata Station - go see the Nanzoin Temple which is stunning. It is totally unknown to all the tourist guidebook "experts" and even many of the well traveled.
https://www.youtube.com/watch?v=lT4VQFmHFyMIf you want to see Gunkanjima (Battleship Island) in Nagasaki, it is an unforgettable place. But if the seas are rough, they cancel the boat tour, so try and get that done as soon as you arrive. If not running, you can try again the next day. There are of course many other good places.
https://www.youtube.com/playlist?list=PL7LcPcmoSg-gbw2yXNLK92siHyNqSNx...Try to go up to Mt Inasa at night for the spectacular view, and be sure to try the chanpon and saraudon while you're in the city.
Kagoshima has some great places, and of course Sakurajima is the elephant in the living room. There is a fast paced one hour bus tour you can take that covers several scenic places to see the volcano. Aside from that, there is the Sengan-en Garden and Shiroyama Park. Altogether, makes a pretty good day of sights.
https://www.youtube.com/playlist?list=PL7LcPcmoSg-irtXXB8IJMdkB9mF0qjn...Lastly, if you like, before going to Matsuyama, you could visit Imabari Castle.