It would help a bit of you gave more info on your interests, as well as you mentioned getting a car from your Day 3 - are you planning to use it for the rest of your trip, or just for that area?
For your Day 2, there is a lot more than Canal City. Try looking through
http://www.thejapanfaq.com/fukpic.htmlPlus if you are hoping to see the cherry blossoms, I'll let you in on one of the best kept secret places in the whole area - if your timing is right, go to see Kayoicho Park in Kasuya, just outside Fukuoka. Extremely few people, and of the best displays you will ever see.
https://youtu.be/pYKNmvevAC4You could also combine it with a visit to Nanzoin, one of the finest temples in the country, yet also a virtual secret unknown to most, even the well traveled.
For your Day 3, the Yutoku Inari Shrine is a good choice. And if driving, the Arita Porcelain Park is not too far out of the way and will be really surreal for you - like leaving Japan and suddenly stepping into Germany for a while.
Regarding Day 4, the Dutch Slope & Megane Bridge are rather underwhelming. But don't miss the Koshibyo Shrine. Dejima is worth seeing too.
In Kumamoto, the castle is still closed. The other big sight is the Suizenji Garden, and well worth it. There are a few other minor places of interest.
For Day 6, it's up to you where to stay, but Takachiho has Takachiho Shrine with its nightly dance. It may or may not appeal to you. You are right that the Aso crater area is off limits. But if the weather is clear and you are driving, there is the Daikanbo Lookout which has a spectacular view. The Nabegadaki Waterfall (west of Oguni Town, down Rte 387) is very nice also, particularly just after a lot of rain. Another delight in the area is the Kuju Flower Park.
http://www.hanakoen.comFor Days 9/10, both are not far from each other; you could stay at either, but Yufuin is a lot more tranquil or dull, depending on your style. Near Beppu is the Takasakiyama Monkey Park & Aquarium, which might be enjoyable.
http://bit.ly/2pZ9opzAnd for Day 11 - there are many possibilities. You could visit Yanagawa with its canal boats, Dazaifu, the Kunisaki Peninsula, Furen Limestone Cave, Usuki stone Buddhas, and lots more.