Transit Card (Suica) - will be your MVP asset in Japan. On the “wallet” app on your iPhone click the plus + icon top right, then Transit Card, then Sucia. Top it up with about 2,000-3,000 Japanese Yen using your Apple Pay.
It’s a basic pre-paid transit card. You can tap on and off all public transport, taxis and pay cashless for items at most places such as convenience stores (konbinis as they’re known in Japan) and vending machines. Great card to save on high overseas bank charges for small purchases. FYI you will still need to book a proper ticket for Shinkansen train fares. 

Cash - Japan is a cash society. Always have cash on you. A lot of establishments, especially small, hole in the wall places will only take cash. When you’re in smaller villages - especially after dark - absolutely make sure you have enough cash. Once at a dinner with a large group of friends we didn’t have enough cash to pay for dinner and the only ATM in town was located inside the post office which was closed! 

Tip: You can always find an ATM inside a convenience store.

Tipping - isn’t common in Japan. If you want to tip, make it explicit when you pay the bill otherwise you might find a very honest restaurant worker chasing you down the street to return your change. 

E-Sim/Wifi - I recommend the E-Sim Airalo from the App Store. So much easier than getting a pocket wifi portal and cheaper than using your existing mobile overseas. 

Book in Advance - Where possible book everything in advance to avoid disappointment. Restaurants, tickets to galleries, shows, exhibitions and long train trips (don’t bother with the JR rail pass; it’s cheaper to buy individual tickets where you need to go). I’ll note in the specific recommendations if you have to book. Ask your hotel to book for you if you get stuck.

Trains - Book long haul trips in advance and make sure you get seating otherwise you’ll end up standing in the toilet section for ages with your bags which is no beuno. The ticket machines at the train station can be a bit overwhelming so I always recommend going direct to the ticket counter and booking in person; they’re used to tourists, all speak English and can help with any concerns/questions - especially helping you on where you need to find your platform. As mentioned above don’t bother with JR rail pass, cheaper to book individual trips as you go. 

Opening Hours - Most shops don’t open til 11am, quirkier more niche places even later. Annoyingly most coffee shops also don’t open til much later either. Check google maps for opening hours for everything to be safe. 

Uber - If you’re not fluent in Japanese it’s better to order Ubers as you can enter your exact address into the app and save yourself and the driver a lot of hassle when you get picked up. Most of the time a taxi will rock up anyway as they’re connected to Uber. 

Luup - Japan equivalent of Citibike, Lime Scooters etc. Download the app and you can hire an e-bike or scooter which is often faster or cheaper than the train or taxi to get places within Tokyo.  

Rubbish Bins - Are not commonplace in Japan. Being responsible for your own rubbish (and most importantly recycling) is your burden and something which is taken very seriously. You’re expected to take your waste home and take care of it yourself. Big tourist areas such as Harajuku and Shibuya will have a few bins and if you’re sneaky you can pop into a convenience store (konbini) to dispose of your items - they’re usually hidden near the straws, utensils and coffee cups.

Etiquette - Talking loudly, listening to videos or music without headphones on the train is bad manners. Same goes for eating/drinking on the train unless you’re seated on a long haul train ride with your own tray table. 
Eating outside on the street is also frowned upon. 
It’s customary to take your shoes off  when you enter someone’s home, some restaurants and all temples/shrines. In-door slippers are usually provided. Take note of separate slippers for restrooms. General rule of thumb if you don’t see signage: Tatami mats = take off your shoes, Historial wooden floors = take off your shoes, Someone’s home = take off your shoes.

Helpful Phrases:
Never once heard a single person say sayonara in all my time in Japan.
The most helpful phrase you’ll learn is ‘daijobudesu’, pronounced ‘die joe boo des’ it’s a pretty broad term but basically means I’m all good thanks / no worries / it’s okay / don’t worry… If someone asks if you want a receipt: “daijobudesu”, would you like a plastic bag for your shopping: “daijobudesu”, sorry I bumped into you: “daijobudesu”, please wait a moment: “daijubudesu”... You get the idea..

Google translate is the best option for most situations but like most foreign countries the effort is really appreciated if you try your best with the local tongue. Who knows you might get a local say back to you ‘Nihongo jozudesu’ which means you speak Japanese well! But it’s also kind of a backhanded sarcastic dig because locals will enthusiastically say it back to you simply for saying Konichiwa 

Here are some other helpful phrases / words: 

*You can piece together some of these to help with ordering a drink for example:

‘Sumimasen, aka wine onegaishimasu’ - Excuse me, red wine please

Konichiwa - Hello

Konbanwa - Good evening

Ohayo - Good morning 

Genkidesu ka - How are you? 

Mata-ne - See you / Bye

Ja-ne - Bye

Daijobudesu - No problem / it’s fine / I’m okay / Don’t mention it / All good / Don’t worry

Arigato - Thank you 

Domo Arigato Gozaimasu - Thank you very much

Sumimasen - sorry / excuse me

Chotto matte - One moment

O kaikei kudasai - May I please pay the bill

Onegaishimasu - Please

Kippu - ticket

Toiretto - toilet

Biru - beer

Wine - wine

Aka - red

Shiro - white 

Mizu - water

Konbini - Convenience Store

Namae wa? - What is your name?

Watashi wa <insert your name>

desu - I am <name>

Izakaya - translates to ‘stay-drink-place’ usually for a traditional Japanese restaurant/bar

Yokocho - means alleyway or backstreets but mostly refers to an alleyway with many bars and restaurants

Ryokan - a traditional Japanese style inn or accommodation

Onsen - baths filled with natural hot spring water, typically located in rural, mountainous regions

Sento - baths filled with regular heated tap water not from a natural source, more common in the cities.

Showa - the period post WWII in Japan during the reign of Emperor Hirohito (1926-1989) during Japan’s insane economic growth, several places in this guide I might refer to as having a ‘Showa era’ aesthetic which is usually a charming mix of Japanese and Western elements which is uniquely distinctive to this era. 

Medical / Emergency / Medications:

FYI - its hard to get normal painkillers in Japan without a script so bring your paracetamol or ibuprofen from home if you think you’ll need it while you’re away. Same goes for Cold & Flu medicine, cannot recommend this enough especially if you’re heading to the snow and get sick because Japanese over the counter medicine is weak AF. On that note do NOT bring Cold & Flu medicine into Japan which has pseudoephedrine or codeine in it as they’re illegal and you can get into a lot of hot water (ie detained) if you get caught with it at the airport. 

ADHD medications are also banned substances and illegal in Japan and can get you arrested.