If flying into Narita, do not get a taxi, the airport limousine service is far better and cheaper. I stayed in Shinjuku and it was 3,100 yen for the trip, compared to over 18,000 for a taxi. The buses don't go to every hotel, but they go to a lot of the main stations which are easily navigate-able.
Get a Passmo/Suica card as soon as you can. This is the Oyster card equivalent. There are machines to purchase them from in nearly every subway station. Depending on how much you plan on doing in Japan, I'd put a minimum of 5,000 yen on it to start. On my first day I used about 1,000. 500 JPY deposit is reserved from your first charge. By returning the card to the teller at the station, you will get your deposit and remaining balance back.
Get used to carrying your rubbish. If you don't know, Japan isn't big on having bins everywhere, and neither is it keen on rubbish. I've walked for about 5 hours on some days and barely seen a single bin, even in the subway stations.
You will be walking a lot. Pack some comfy shoes and bring lightweight clothing with you.
Download the Japan WiFi app. Link below. Chances are you're going to spend time on a train this trip, but fortunately, most stations have wi-fi (that I've experienced) and many other places have wifi access through this app, helps relieve some boredom.
http://www.ntt-bp.net/jcfw/en.html
Take a lot of water with you. You'll be spending some time on the subway systems and the air gets quite dry. Keep yourself topped up to avoid headaches. It's only 130yen for a 555ml bottle of water.
Shops aren't open as much as you'd expect. The opening hours of most shops is between 10am and 5pm, but for some it's 11am. This is a little restricting if you want a whole day shopping including lunch, but fortunately food is quite quick to arrive so it's only about 30 mins max out of the day.
Learn the customs part 1: Restaurants. You're going to be given chopsticks. They won't automatically assume you can't use them so if you can't you'll have to ask for a knife and fork. As for using the chopsticks, when finished with them, lay them at the edge of the table closest to you, likely how you got them. Do not cross them or stick them upright in food as these are more associated with funeral customs. Do not tip, even if you think "Wow, this was amazing and the service was great" you still don't tip, it's almost seen as offensive to do so.
Learn the customs part 2: Manners. You'll go far if you remember to say "Arigatou Gozaimasu" when you finish buying something or leaving a restaurant, or asking for information. With regards to the bowing culture, if unsure how much, just go with a gentle head nod. If they reciprocate with a full bow, then copy that. On the flip side, there seems to be no issue with personal space and I've had a few people walk into me without so much of a "Sorry" so be aware of that. When in public, sneezing, coughing, sniffing are all fine, even without covering your mouth, but blowing your nose is not the done thing (from what I've heard anyway). If you're a smoker, 99% of the time there's no smoking anywhere, even on the streets. There are designated smoking areas everywhere (even inside train stations) so keep your eye out for them.
Roads. Chances are, where you live, when you cross the road, the traffic coming your way stops. This doesn't happen in Japan. The signal to cross will be green, however, cars can still turn left into the road you're crossing, but you still have the right of way. The Japanese also drive on the left hand side of the road.
Language. You're going to understand basically nothing they say to you, but there are a few phrases that will prove helpful.
Ohaiyou Gozaimasu - Good Morning
Konichiwa - Hello
Sayounara - Goodbye
Yoroshiku Onegai Shimasu - Nice to meet you
Arigatou Gozaimasu - Thank you
Sumimasen - Excuse me (very useful in shops)
Hai - Yes
Iie (pronounced e-yea) - No
Eigo - English (when asking about menus in a restaurant this is very helpful)
Nihongo - Japanese (I've been asked once or twice when it comes to explaining things)
NB: If a word ends with an 'su' (Gozaimasu) you don't pronounce the 'u'
Money. All coins have their value displayed on them, except for one. The goldish coin with a hole in the middle is a 5, the only other coin with a hole is the 50 so they'll be easy to differentiate.
Bank Card. If your bank card has Plus, Cirrus or Union Pay logo, it has good chance to be accepted by the ATM in the Post Office or 7-11. You receive Japanese Yen and equivalent balance is debited from your balance. I had a visa debit and credit card with me and this hasn't been accepted at some ATMs, but they all list what they accept on them so just double check first
Tall people. In Japan, if you're over 5'10" you're going to find youself ducking a fair bit. Train doors are a lot lower than you might be used to, and the showers in hotels are only about 6'6" high to the ceiling, which causes issues when washing your hair.