Probably the best way to learn what to expect if you visit/move to Japan is to find someone to talk to that either lives there now, or has lived there recently.
Here is some quick info, that is not exactly traditional culture related, but more for the everyday visitor/resident of Japan:
1. If you do not like walking, you may want to change that. Unless you plan on paying over $10 US just to take a taxi to the next block
2. Trains/Subways are the worst on Sundays, after 6pm, before 10am, and during lunch hours.
3. I would recommend not going out on Sundays unless you like hearing high-pitched ladies yelling for advertising purposes, waiting in a line as long as opening day at a theme park just to get a hot dog at Costco, or not being able to see your own feet because the stores are so crowded.
4. The best times to visit are spring, when the 桜 (cherry blossoms) are in bloom, and early fall when many Japanese festivals are. I would not recommend visiting in the summer or winter when it is too hot/cold to really do anything. Unless you plan on going to Hokkaido of course, then summer is beautiful there.
These things may not be 'culture' per-say, but they can be just as important as when to bow, or where to take off your shoes.