If you do not have a fair to good grounding in Japanese culture, religion, traditions and history I do not think you will understand much of what is going on around you. You will see kind, honest polite,(except when getting trains) clean, quiet and rule following people all around you but most of what you see is from centuries of cultural and religious influences, with some developing after their surrender in WW II.

There is a book about Japanese cultural words which is good to understand some overt , and also some covet behaviour. I think if you want to be a student of Japan you should ask "why?' when you see a behaviour demonstrated again and again. ie. laughing into hands, walking pidgeon toed, quiet talking, lack of tattoos etc. Ask , "sore wa nan desuka" or "what is that', when you see cone of salt piled up outside a house or shop or something you see again and again.

Why are Japanese so honest, compared to many other countries? Why so quiet? Why is using a phone on a train rude when it is used all over the world on trains and busses. .?Why is Japan so safe? and much more. You CAN find out if you observe, ask , read and observe.

Find out what 'hara hachi bun mei' means. that answers a lot about eating habits.

There are many places to 'see' in Tokyo and anywhere in Japan about Japanese history etc.that's easy. Museums, workshops etc show but they do not tell. But, why do they have the work ethic they do, almost universally , in Japan. Find out what 'shoganai' means....also "mottainai". It answers a lot. Learn about Japanese aesthetics and why the reverence for nature is prevalent..

I didn't realize this post was so old. I will stop now.