Here are some tips I normally give to foreign visitors to Japan:
1. You do not need to tip in hotels and restaurants. Really. It is not expected at all, and good service is included in the price already.
2. Although people in Japan are generally very educated, most of them do not speak English very well (compared to, say, Hong Kong or Singapore) So if you ask for help in English, it is better to speak very slowly or write the question down. You might get answers. Younger people tend to speak better English.
3. If you do not look like a Japanese and if you visit some small village, you may get stared at for their curiosity, not hostility. So you might get used to that idea (although this aspect is getting better as more and more foreigners are visiting Japan nowadays).
4. Japanese people are generally shy and polite. They may not make eye-contact when you talk to them. Please don't think they are impolite or not being truthful. It's just the way we communicate, especially with people we do not know well.
5. If you have a tattoo, it may be better to hide it as it is often frowned upon, unfortunately (often associated with Yakuza, Japanese mafia). Some Onsen (hot spring) or public bath may refuse your entry because of it. Check first.
6. Most streets do not have names. So finding places could be tricky. Normally people give directions from a good landmarks. Ask the police officers for direction any time because that is one of their jobs to help people find places :-).
I hope these tips help :-)