Many of the sites in Mojiko are within walking distance of the JR station. Of interest is the Kyushu Railway History Museum where you can ride a toy-like rail engine, a treat which children will love. Another unique site is the Shimonoseki-Mojiko Tunnel where you can walk from Kyushu back to Honshu. The tunnel is reached by 10-15 min bus from the JR station.
http://www.retro-mojiko.jp/english/index.htmlThe best way to enjoy Yanakawa is to take a canal punt. Another thing not to be missed there is the popular Unagi eel on steam rice.
http://www.yanagawa-net.com/eng/index.html Information on "99 islands" cruises:
http://www.pearlsea.jp/english/cruising.html Sand bath in Beppu:
http://www.hyotan-onsen.com/pdf/english.pdf Sand and mud baths in Beppu:
http://www.beppu-navi.jp/ml/english/hotspring.htm Apart from the touristy "hells" in Beppu, make an effort to go for the site shown in the following blog and try out the "hell pudding"
http://www.wretch.cc/blog/bearpalm/14748500 http://www.japan-guide.com/daily/?040419 Kyushu has so much to offer that it is hard to pick for a 6-8 days itinerary. Without rushing too much, your initial idea of concentrating on the northern region is a good idea. Save the south for a future trip.
Without going further south from Takachiho Gorge, sites worth considering in the north IF you still have time are: Kokura, tea plantations in Yame area, Usa Jingu, Usuki Sekibutsu Stone Buddhas, African Safari Park, Kokonoe Yume Otsurihashi suspension bridge, Aso Refresh Resort and Genki Forest, Mitsui Greenland Park and Ultraman Land, Tsujunkyo Aqueduct/Bridge, Cuddly Dominion Zoo, Shimabara, Unzen, Sasebo, Arita, Imari, Karatsu, Yobuko, Ureshino Onsen, Saga, Yutoku Inari Shrine, Yoshinogari Historical Park, Tosu Premium Outlet, etc.
The list is long and it is far from exhausted. You have to choose according to your interest and available time. Depending when you are going, there are flower parks and u-pick fruit farms that are opened for visit if the season is right. Also there are seasonal events and festivals that are worth going for if they coincide with the time of visit.