Itinerary Check

Hi,
I think you've done a great job planning your itinerary. Going from Matsumoto to Takayama would have to be paid out of pocket for the bus (¥3190) but saves you a lot of time. You might find Takayama these days to be a bit too touristy. If so, then go up a bit to Hida-Furukawa for a lot of the same atmosphere without the tourists.

One thing I might change is that since you are already going to see Tokyo, Osaka is rather redundant, and I noticed you have not listed Himeji, which has Japan's best castle. Keep Osaka for the evening after the temples in Kyoto close around sunset.

For Hiroshima, you might fit in Miyajima and Iwakuni as well if you like.
Fukuoka is sadly an often ignored city and some just use it as a jumping off point. But there are many good places to see, which you can listed here. The Nanzoin Temple in particular is extraordinary, yet so unknown that the tourist guidebooks and online guides have never discovered it. If you can fit it in, a day trip to Nagasaki is also very worthwhile.

The rest of your itinerary is a bit murky. I don't know what you plan to see in Kanagawa, Atami (although Izu is great), Shizuoka or Tochigi. For Kamakura, you can also include Enoshima for some very good scenery.
For your time in Tokyo, you can use a 2 or 3 day subway pass and if you're using Narita, there is the 1000 yen bus.

Good luck.