If you've never been to Japan before and truly want to go, there are a handful of undeniably helpful recommendations that I can suggest.
1. Japan is a city that is based on walking. If you're planning to pack your luggage as if you're visiting EPCOT, think again. Pack light, pack simple.
2. If you are not a walker (and prefer the use of taxicabs), either change your travel plans or bring an additional $400 for cab fare. Japan is a city that revolves around people who can easily get aroudn on their feet. If you don't plan to travel on foot, you're in for a big surprise.
3. Allergies and Preferences - always bring a small series of cards that you can print at home that reflect your personal preferences - allergies, gluten-free dietary habits, etc. Don't assume that a waiter or waitress will completely understand your request. Handing the waitstaff a simple card that says, "I'm allergic to nuts. Please ensure that my meals do not include nuts" will make a remarkable difference in your daily culinary experiences.
4. Japan LOVES recycling. You won't find public, general waste/trash cans. Everything is recycled - yes, everything. If you're expecting to toss your trash in a common-area waste can, they don't exist. A great example - the burnable waste (newspapers, papers, magazines, etc) in the city of Chiba, Japan is often used to burn beneath the public swimming pools to keep them warm.
5. Vending Machines are everywhere - prepare to always carry a handful of change while you're walking through the streets of Tokyo. On average, there are 100 vending machines in nearly every 4 block area. That's a lot of vending machines.
6. Never tip anyone - don't be prepared to tip cab drivers, doormen, waiters or anyone else. It's deemed to be rude and unacceptable.
7. Don't yell or speak loudly in subways. You'll notice that the subway cars are usually quiet. Many people (Japanese citizens) sleep/nap while getting to their destination. You'll find that most commuters in Japan play on their smartphones or read. Most do not speak. They do this to be kind and considerate for those who are attempting to get some shut-eye. By speaking, laughing loudly or yelling on the train....you'll stand out like a loud, obnoxious American.
Master/Remember these seven tips and you'll do a lot better while enjoying Japan. Trust me. :)