I have been following this thread for a while, just never get around to posting. I am an American ex-pat who has been a resident of Japan for nearly ten years. I am glad to see you are having a nice trip.
If you find yourself, in the northern parts of the country, (the Sea of Japan side), let me know I would be happy to show you around and take you to some places.
I will second the recommendation, if you have the chance please visit Nara and Kyoto they are well worth the time and effort to get there. I will be spending the Holidays at my inlaws in Shizuoka. I will base myself out of there doing some shooting around Mt. Fuji, and Tokyo. I might go to Kyoto for a day. If you are heading up that way, feel free to drop me an email and I would be happy to take you to some places that I know.
Have a nice visit!