The Japanese, for the most part, give you the benefit of ignorance.
Even when I broke 'rules', nobody was particularly upset.
When in Japan, do as the Japanese do... Be very respectful and pay close attention to Japanese mannerisms --
But as far as individual do's and don'ts, I cant really think of anything in particular...
Halfway in my trip I realized that no Japanese people ate while on the train, walking, etc... So as I was lugging around drinks and snacks, and tons of trash, while everyone else was doing the opposite.