It's really a shame you'll only have 3 days in Tokyo, especially if you consider yourself a "Japanophile." Tokyo alone could take a month; I was there for 9 days in 2015 (out of a 2-1/2 week total trip) and feel I didn't see enough of it.
As a westerner, particularly coming from the US, one of the things you'll be shocked about is the attitude towards customer service, regardless of position. Your lowly 7-11 clerk will be just as polite to you as the waiter in an expensive restaurant. Oh, and no tipping! Employees are expected to give the best customer service regardless of whether or not you "bribe" them, and some Japanese actually find tipping to be offensive.
Another thing you'll be shocked about is how clean everything is. I saw almost no graffiti there, not even in Tokyo. Japanese are a fastidiously clean people, and they often will carry an empty bag with them (usually the one they got from the convenience store) to put their trash in, and yes they will carry that around with them until they can find the proper place to dispose of it. They're also fastidious recyclers, and even at McD's you'll find different bins for different materials to be disposed of, and yes you'll be expected to use the right bin.
For your short time in Tokyo I'd book a bus tour of the city on your first full day, to give you a brief overview of it. You can then go back to whatever areas you had a greater interest in. I recommend using the Hato Bus tour line: https://www.hatobus.com/
and yes they have tours with English narration.
Speaking of tips, a few more:
1. Narita Airport is a long ways from central Tokyo. DO NOT TAKE A TAXI from this airport all the way into Tokyo, you'll be paying a fortune. There are two express trains, the Narita Express (run by Japan Railways Group or JR) and the Keisei Skyliner (run by Keisei , a "private" railway which is a bit of a misnomer as the JR Group is also privately run, though it was once government-owned). Narita Express or N'EX is best for accessing points along the southern, eastern and western sections of the Yamanote Line "circle" particularly if Tokyo, Shinjuku, and Shibuya stations will be your destination. Keisei Skyliner is better if you're staying in the northern part of this circle such as near Ueno Station where I stayed. The Yamanote Line is the rail line that runs in a circle (more like an oval actually) around central Tokyo. If you're staying in a hotel that typically caters to westerners rather than Japanese, there may be a direct bus from the airport to your hotel, called a "limousine bus" provided by a third-party company. Check with the bus desk at the airport.
2. While I discourage using a taxi from the airport, it is well worth the money to use a taxi once you get into central Tokyo by train. The regular commuter lines aren't built for large amounts of luggage and they can get quite crowded. There is a popular and rather inexpensive luggage delivery service called "Takkyubin", and they have an office at the airport near the meeting point, but if you do use this don't expect to see your luggage again for a day or two, so make sure you have a small bag with a day or two worth of essentials. If you use a taxi, it's best to have the phone number of your destination, or a printout of their address; Japan uses a very strange and confusing addressing system that makes no sense whatsoever to westerners. GPS/sat-navs in Japan have the ability to take you somewhere based on its phone number. Taxi drivers typically do not speak English.
3. For getting around, buy a refillable transport card. For Tokyo there are two types, the "Suica" and the "Pasmo." The former is administered by JR, the latter by the Tokyo Metro subway. In the Tokyo area they are pretty much interchangeable, and are also good on most transit buses. You can buy and refill them at the train stations and most convenience stores. Some stores particularly those at or near train stations will even let you pay for your purchase with a Suica/Pasmo, and some vending machines will also accept them.
4. Money. Despite its reputation for being high-tech, Japan is still very much a cash-only society. Except for places that cater specifically to western tourists, or the Ginza shopping district, you'll find credit card usage to be difficult. Japan is a very safe place so it's not unusual for locals to carry the equivalent of a few hundred dollars at any time, and some ATMs will dispense as much as 100,000 yen (roughly $900 US) at one time. Speaking of which, the only ATMs that will accept cards from American banks are the ones at 7-11, at the Japan Post office (they have a symbol which looks like a "T"), and at the few Citibank branches in the country.
5. Almost all restaurants have plastic facsimiles of their menu in the front window, which is helpful because most menus will be in Japanese and the servers are unlikely to speak a lot of English. So take a photo of whatever you would like to eat and show it to the server. Many restaurants will also have picture menus but not all.
There are many travel tip websites and videos on visiting Japan, and I would recommend viewing them. I would also recommend the YouTube channels of these two western expats: "Rachel and Jun" who are an American-Japanese couple, and "Abroad in Japan" is a Brit named Chris Broad who came to Japan several years ago and has documented his experiences here. Some of the latter's videos may not be safe for work as he does have a bit of a potty mouth; indeed his funniest video of all is possibly the one where he actually teaches English profanity to Japanese. This video from Attaché also has some good tips on coming to Tokyo:https://www.youtube.com/watch?v=GdIaEL72PwI
Feel free to ask me more questions. When I was there I met up with cwerdna for the Tokyo Motor Show and he's been to Japan a few times, I'm sure he'll have other tips as well.
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