I'd agree with everything Gerald_Ford wrote.
He beat me to it about taking books on Japanese culture with a critical eye.
Many are about "doing business" with the Japanese. Many are also of the what I did on my summer holidays, isn't Japan strange or isn't it dreadful because it's not my culture, type.
That said I'm a sucker for all books Japanese!
I found 2 that are interesting. Both written by Japanese.
Japanese Cultural Encounters by Hiroko C. Kataoka
This bookk gives 56 short narratives or situations then you choose between 4 explanations of what was happening. The answers are then briefly discussed.
I think it was meant as a starting point for classes about Japan.
Traditional Japanese Culture and Modern Japan by Yoiichi Sugiura and John K Gillespie 1993
This is a bilingual text. I don't even know if it is still in print as I found it second hand. The modern stuff might be a little dated but a lot of it is about traditional customs. And tradition is still quite strong in Japan in my experience. It gives a deep background to what you might see going on.
On the Internet the Daily Yomiuri english edition has weekly essays.
http://www.yomiuri.co.jp/dy/features/language/
Behind the paper screen is one such and cultural conundrums is another.
Unfortunately access to their archives is a paid service.
Japan might be a culture shock no matter what. Well that was my experience at first.
It's the practical day to day stuff that is seldom written about that would have been useful. And when misunderstandings occured I doubt a book would have helped.
If you have some friends who can help you or give you an "in" into the real culture it's much better and gets more interesting and gives you more confidence in exploring Japan. (I may never have started going to onsen if I wasn't taken to one by a friend. And even once saw some Yakuza in a 1950's era sentou once. scary guys, but neat tattoos.)
I'd add another rule. If you get the chance join in.
With the corollary, while at times there is comfort in your own culture, don't just be part of the ex-pat culture. Off the beaten track you meet much more interesting people.
I'd also recommend just general reading. Read some history, (especially post 1945). Read modern novels (by Japanese) Even watch TV dramas or films (daily life sort of thing) Bearing in mind that they are drama you can still learn a lot.