This may be controversial, but I have read a lot of the Japanese etiquette handbooks and materials and I don’t worry too much about this. There is no way I will ever be a Japanese person -- I will always be a Western person living in Japan. Every Japanese person I know is very forgiving of any cultural gaffes or faux pas that I commit. No one in Japan expects Westerners to act Japanese. And in fact, for almost every one of the “rules” I see, I have seen Japanese people ignore that same rule. 

So, the rules that your read about, they seem more like guidelines than rules. For the most part, if you are polite, not pushy, and patient, you won’t have any worries.

I do have a few guidelines that seem more critical than others --

Business Cards: These are widely used, even in personal situations, and I highly recommend both a business card for work-related activities and a personal “family card” for other connections if you are here with your family for an extended period of time. 

Loud teenagers: In Japan, loud teenagers are universally frowned upon, or in some cases, spoken to or even attacked (it happened to my son’s class on a field trip). This appears to be for any teenager, not just Western teenagers, but Western teenagers are generally a level or two louder than Japanese teenagers as a rule. This probably applies as well to running, general “goofing”, and other physically obnoxious behaviors which are very seldom seen among Japanese young people. Loud kids should definitely be more quiet and restrained in public circumstances.

Loud or obnoxious adults are probably just as bad, but maybe not as common. Update: I now have seen a loud obnoxious woman on the subway. She was apparently upset at another passenger, I’m not sure why. It may have had something to do with who had to stand and who had to sit down. If I had to guess the conversation was something like, “Who do you think you are to try to take my seat?” Only one person was loud, however. Pretty much everyone in the subway car was surreptitiously looking at her with a look of disapproval. I highly recommend that you avoid being loud on a subway.

Chopsticks in rice: Don’t stick your chopsticks (in Japanese, hashi) vertically in a bowl of rice. This is usually done as part of a Shinto ceremony for the dead. The forgiveness rule probably applies here as well but I have never ever seen anyone Japanese do this, so best to avoid this one.