For Kyushu, make use of the link to work out the places to visit. Nagasaki & Mojiko are very nice places with European influence. Yuifeni is a scenic little town. Staying there can be expensive. Aso- did not go on my trip there cos of time constraints.
Take the Trans-Kyushu rail that run east-west.
You may go north to Honshu to include Himeji & Hiroshima/miyajima if time permit.