There are a couple of things you may not be aware of regarding your plans. The first is with the Sanyo San-in Northern Kyushu Pass. You can start using it from Maibara, but the bullet train coverage only starts from Shin-Osaka. It's up to you if you want to buy a bullet train ticket over to Shin-Osaka to save time.
Also to get to Beppu the quickest, you'd switch trains at Kokura (Kitakyushu), taking the Sonic Ltd Express train. One other important thing is you can't buy JR West Passes in their ticket offices anymore. You'll need to get the exchange order at a travel agency before departure, or order it online. You might want to look at all the official info before your trip:
https://www.westjr.co.jp/global/en/ticket/pass/ssnk/You are also looking at some very long legs - using the pass like you suggest, getting to Beppu will take close to 5½ hours, and Beppu to Aso is about 4 hours. You don't say what you'll do, though the main draw of the place is the hot spring experience, as well as the Hell's Tour. The latter you can do in a few hours, so timewise it'll work. But there are some other good sights nearby, like in Oita City the Takasakiyama Monkey Park is one of the better ones of Japan. Seeing a place that has hundreds of monkeys around you is not something most people can do easily. For Aso, I wonder if you are up to renting a car for the area - it would be the most convenient by far, and there are many good sights in the region. Aside from the crater rim, the view from the Daikanbo Lookout when the weather is good is tremendous, and Nabegataki Falls is a nice place to see also. Kamishikimi Kumanoimasu Shrine is also a cool place to visit, and if you can stay in Kurokawa, it offers some very nice outdoor forest hot springs that are not that too common elsewhere.
The main sights of Kumamoto are the castle and Suizenji Garden, plus a few other minor sights if interested. You are putting in some good time for Nagasaki though. Actually, if you can see the Yutoku Inari Shrine on the way there, it is one of the finest Inari shrines in the country. If you do go to Gunkanjima, you will need that time there - it takes 3 hours by itself, and that just has one hour on the island. The boats could be closed for the day if the weather is bad, so be sure to have some other back up plans. You might also consider seeing Unzen (again, renting a car is by far the better way to get around), or going to Sasebo - Huis Ten Bosch is the most famous, but the 99 Island cruise is also quite nice and if you get good weather and can see the bay from several overlook points, it will surely be a highlight of your trip. Nagasaki has some excellent food as well, like chanpon, saraudon, and the Sasebo burger, so by all means try them all.
For Fukuoka, be sure to see the nice Nanzoin Temple just outside the city. You also might want to see Ohori Park (see the traditional garden on the south end as well), TeamLab Forest, and Fukuoka Tower. Outside the city is Dazaifu, Yanagawa, or you might want to see a bit of Kitakyushu or Mojiko.
https://goo.gl/Q843Bg
