Definitelt try to get to Mt Aso at some point. There are some lovely spots in Kyushu. I think there's some old bloke lurking in this forum who might know more than me though.
On Shikoku try and get to Kochi on a Sunday for the market. Never failed to enjoy myself there. The coast from Matsuyama all the way around to Kochi city is quite nice. Cape Sada has some choice views. Think about renting a car.