That is awesome, I hope you enjoy the trip. Go in with a clear mind and no expectations other than it being awesome and you will love it.
In my travels thus far. Kyoto is still I think my favorite city followed very closely by Hiroshima. I definitely suggest going there and spending the day visiting the Peace Park which is free if you have the time. The city is not only gorgeous but the energy there, though heavy, is really uplifting once you get acclimated to it and face what history is there. If you and your girlfriend are sensitive, I would suggest skipping the Memorial Museum however. It proved too difficult for me to get even a quarter of the way through.
As far as places I make sure to visit, I love hiking Fushimi Inari in Kyoto. The Torii gate walkway leading up makes you feel transported to another time, similar to walking in the bamboo forest of Arashiyama. And the view is breathtaking towards the top, it is not for the faint of heart though. It is not uncommon to see people turn back part way up because the altitude can get you tired quickly. Bring water and comfy shoes. I am a sucker for being in nature these days, so anything outdoors I will always make time to do.
I am a practicing member of Shinnyo-en Buddhism, so Yuon and Shinso-ji in Osaka and Tokyo respectively are wonderful places I head back to to spend some spiritual time to myself or with my family.
It sounds like a waste, but go see a movie in Japan. It is a really cool experience ( I was a film major so the film nerd in me was geeked to finally do so). There are various Toho Theater Complex's over the country and the Aeon chain of malls usually has a theater as well. Be warned it is quite expensive to see a film in Japan (around 1800 yen, or about 18 dollars) and that is just tickets. They do have pretty cool food items that are uniquely Japanese for the theater and they sell cool theater only film related souvenirs inside so you could pick up a memento while you wait to be let in.
If you dig stickers or buttons, you have to check out B-side Label. It is one of the coolest stores I have been in, I could spend hours and hundreds of dollars in there. wall to wall stickers and buttons. I have been to the Teramachi location in Kyoto and I go out of my way to visit and spend some when I do. They also have various styles of stickers available at Village Vanguard's all over (think Spencer's, Hot Topic, and Borders but way more awesome) and each city has exclusive sticker styles. In Osaka they have Hanshin Tiger (a local baseball team) and Tako (octopus) theme ones because Osaka is known for those. Oh and Rumiko Takahashi's character, Lum. Takahashi hails from the city.
Sorry, I could talk forever about Japan and never get tired of it.
