The Japanese are extremely respectful. So you will be expected to make every effort to respect customs and be polite during a visit to Japan.
There are fundamental differences between the west and east when it comes to food.
Despite high sales of takeaway food, eating in the street or in public places is frowned upon (and sometimes even banned).
During meals, you should not pour yourself a drink, but fill the glasses of others when they are empty, then wait for them to do the same for you.
When it comes to using chopsticks, the list of things to avoid doing is quite long, but here are the main points: do not pass food from your chopstick to your neighbour's (but place it on his plate), and never put chopsticks upright in rice (this is used in funeral rituals)!
Also, making a noise whilst eating is not a problem, so being too quiet could appear strange.
When you go into someone's home or into a religious building, you take off your shoes, and put on the slippers provided.
Homosexuality is relatively well accepted, but displays of affection in public (holding hands and kissing) are frowned upon, whether it be between homosexuals or heterosexuals.
A final word, the Japanese almost never say no. As a result, it is not always easy to see whether you have caused a problem or not, it is up to you to decide and act accordingly. If however, someone hesitates or says no, never insist as this would be very impolite.