Some you just cant avoid. Without living there for years or going with someone who does it is inevitable. However, I can offer this advice, a lot of how your treated afterwords depends on where you are and who you are around and what you did. Think about it, in most english speaking countries people have a wide variety of ideas about table manners, some people ignore tiny infractions, some people dont. Depends on if you are in a home, nice restaurant or mcdonalds. Its kind of tough to generalize about making "cultural" mistakes.

that being the said the Japanese, in my experience, in general public are very understanding of mistakes made by foreigners because they are aware of the differences in culture, same as you are before you go. Dont be afraid to ask if you see someone make a face would by my advice. They are happy to share for the most part.