I lived in Japan for a total of 3 years for work (2 sperate periods).
I have a bunch of photos on my flickr that will give you an idea of a lot of different areas, some often not commonly travelled to by tourists. Most of them should be labelled or tagged with the location (no GPS though)http://www.flickr.com/photos/davidcampbellphotography/collections/72157608783712689/
I would highly reccomend using www.japan-guide.com
for research, there is a lot of good content on there.
During september, the autumn leaves will be turning in higher latitudes and higher altitudes. Autumn is my favourite time in Japan. This website, as you get closer to the trip will give you an idea of the autumn leave progression. http://kouyou.yahoo.co.jp/
it is in Japanese but you should be able to put it through google translate.
If you are into Landscapes, Kamikochi in Nagano Prefecture has a lot to offer.
Nearby is Matsumoto that has a stunning original castle. This town also has a woodblock print museum where you can buy nice original process hand made wood block prints/replicas of more famous works.
Also Nearby is Takayama, Shirakawago which have traditional grass hut villages.
Kanazawa has a stunning garden, nice geisha/gold leaf district as well as a cool "ninja temple" called ninja dera. Basically a temple with many levels and hidden doors etc.
I also reccomend the following places Nikko, Koya san, Nara, Kyoto, Kamakura, Hiroshima/Miyajima, Sendai/Matsushima.
In Kyoto, there is an un written rule that you cant use tripods in/around the temples. I used to get told off a lot as many places dont have signs.
Good luck with the trip planning.