I'd switch things around a bit, taking a day from Shimabara and adding it to Nagasaki. If you go to Nakasaki first, you could follow that with the drive over to Shimabara. When done there, I would take the car ferry across to Kumamoto, continuing the trip from there.
I also agree with the suggestion to add a day or two to Fukuoka/Hakata. It is an interesting city, with some hidden gems.