[Firebird]

Looks ok to me! I think you could fit in the Museum on the last day with Odaiba. From there you can walk through a nice park (inokashirakoen) towards Kichijoji wich is where lots of locals go to hang out or for shopping.

Doing Himeji and Miyajima in 1 day is possible but i would do Himeji in the morning, than go to Hiroshima and see the A-Bomb dome (the Museum is great as well) and stay there for the night. The next morning visit Miyajima and than drive on to Fukuoka. Fukuoka is a really nice city, might be worth an extra day!
When going to Beppu stay in a traditional Ryokan and take the Bus to the Hells, its really worth it (go to the ones the tourist information recommends, the other are not so good).
What is your plan for Nagasaki? I have been there a day but theres not to much to do.

If you want to do something a bit crazy you could jump over to Korea with the ferry (3h one way) for a day or 2. The ferry goes from Fukuoka to Busan and the visa is no problem.

Otherwise the nightview from the mountains around Kobe is really nice, so you could spend a day around Osaka and have dinner in the Kobe Harbour Area, than drive up with the cable car to see the nightview of Kobe and Osaka (japanese say it a million dollar view).

Have fun