Help with Kyushu itinerary would be most appreciated.

Hello and thanks for reading my post. I have been revising my Shikoku-Kyushu itinerary, particularly the Kyushu section, and could really use some help now. This trip begins and ends in Tokyo as my travel companions wish to spend time there on arrival and departure. We will be using JR pass (14 days all of Japan) and will travel in July 2017. This will be our 4th trip to Japan but first to Shikoku-Kyushu.

Arrive Tokyo for 4 nights.

Tokyo to Takamatsu ( begin use of JR pass) on overnight train for 3 nights including day trips to Naoshima and Kotohira.

Takamatsu to Nagasaki for 3 nights (7.5hours) including day trip to battleship island.

Nagasaki to Kumamoto (3 hours) for 1 night.

Kumamoto to Mt Aso (if possible) by Kyushu Odan Bus in early morning (1.5 hours) then on to Kurakowa Onsen on Kyushu Odan Bus mid-afternoon (1 hour) for 2 nights.

Kurakowa Onsen to Beppu on Kyushu Odan Bus mid afternoon (2 hours) for overnight ferry to Osaka then on to Kyoto for 3 nights with day trip to do Magome - Tsumago walk - possible to do this as day trip?

Return to Tokyo for 1 night and departure or possibly direct to departure.

Thanks for all recommendations and feedback, most appreciated.