As I wrote previously, I think you need to check the times of the various flights and trains and see what works best for you.

Hyperdia is a good resource for finding out what's possible in terms of domestic travel by rail and air.

Depending on the arrival time of your flight from HKG, you might want to look at the possibility of connecting at NRT to a domestic flight. There aren't many domestic flights out of NRT, but it's possible to get to CTS, FUK, and HIJ, for example. I think that any of those places would be quite a handy start point for the trip you're planning. (Alternatively, it might make sense to end your trip in one of those places - and get a flight to NRT that lets you connect with your international departure).

Another thing that you might want to consider is using a JR pass for some of the more expensive rail trips you might make - That means bringing together some of the expensive train journeys into one period.

I'd also recommend grouping the time that you allocated for the Osaka/Kyoto region (rather than sandwiching Himeji annd Hiroshima between Osaka and Kyoto) and leaving your plans flexible so that you can change your mind if you find one place particularly interesting. (Osaka/Kyoto/Nara/Kobe are close enough together that you could use Osaka or Kyoto as a base to explore the whole region).

Time to hit the timetables....