Here are few things that are considered rude in Japan. I think if you just know theses things, traveling in Japan will be easy.
Stay on the Left
Everything is the opposite in Japan. Even the escalators.
In the States, we stay on the right. In Japan we stay on the left.
I kept forgetting and stood on the wrong side like an annoying tourists.
Make Sure You Bring Enough Cash
Even though most countries are moving towards credit cards and tapping, Japan is still heavy on cash.
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Even a famous Michelin restaurants would just take cash. The guy behind me stood on line for 30 minutes and found out, the restaurant only takes cash. He had to leave.
Stand on the Green Line
Make sure to stay on the line it says to stay when you wait for the subway.
Tokyo Pass Will Make Your Life Easy
Tokyo metro is so confusing. This thing is not considered rude in Japan, but I just wanted to let you know how your life can be easy with Tokyo Pass.
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Trust me. Tokyo pass will make your life easier.
Take Your Shoes Off
Many places will ask to take your shoes off.
Restaurants where you sit on the floor or hostels.
If you just go in with shoes.
There is a blogger who gave 30 different things that are considered rude in Japan. I think this is a bit excessive, but still can be useful I think.