Train Travel in Japan
My plan was to land at Narita and then take the Narita Express to the Shinkansen at Tokyo Station and head to Kyoto. From what I gather, this is not a usual plan regarding travel in Japan. Most travelers seem to land in Tokyo and spend a few days there before heading elsewhere. I can see why.
Shinkansen trains of all tiers run all day long, and if you are leaving Tokyo in the morning you have seemingly infinite options in a full range of prices. My plan to leave right after an evening arrival in Tokyo added an extra level of stress to my trip, seconded by the alarmed look the JR official gave me when I informed her I wanted to go to Kyoto that night. It wasn't impossible, but had anything gone wrong with my plane travel I would have had a serious wrench thrown in my plans. As it was, upon landing, I had to clear customs, pick up my portable wifi, buy tickets for both the Narita Express and the Shinkansen to Kyoto, then make the Narita Express, then find the Shinkansen tracks at the station and not miss that train. In practice, none of this was difficult, but as a to-do list in an unfamiliar airport and country on the first day, it was a tad overwhelming.
JR Rail Pass
Most guides I read and people I've asked about Japan will recommend the JR Rail pass, which is a voucher available to foreigners traveling to Japan, exchanged for Shinkansen tickets between cities and used for all JR subway lines in major cities. The fine print of this pass is that you have to buy it before you head to Japan, and you have to buy it with enough lead time that they can FedEx you the voucher. Why it isn't electronic, I have no idea. I didn't realize this was the case, and so I sat down to purchase two days before my trip to Japan, too late to buy the pass. So if you want to purchase this and use it, make sure you do it at least a week before you are heading to Japan.
The other fine print of the JR Rail Pass is that it only covers up to a certain tier of Shinkansen. It actually worked out that I wasn't relying on the pass, because landing in Tokyo with limited hours until trains stopped running, I needed all options available to me. I ended up purchasing tickets for the Nozomi Shinkansen, the fastest but most expensive Shinkansen ticket (go big or go home, right?). This would not have been covered by the JR pass.
Where the JR Pass really saves you money is if you are traveling between multiple cities. My roundtrip to Kyoto was comparable in price, but had I also decided to go to Osaka, then I would have been spending more than if I had purchased the pass. The JR pass can also be used on all JR subway lines in all major cities in Japan, but my experience traveling around Tokyo and Kyoto proved that JR lines were rarely the subway lines I needed to take, so I would have been spending extra money for subway trips on top of the pass.
Shinkansen (Bullet Train) Tickets
Purchasing individual Shinkansen tickets was incredibly easy. There is a JR or Shinkansen ticket office located in all major train stations and airports, and the staff speak English. I walked into the JR East office in the lower level of Narita Airport, and 5 minutes later walked out with both my Narita Express ticket and my Shinkansen ticket to Kyoto. I booked the return separately, because I didn't know exactly what time I planned to leave Kyoto to return to Tokyo, but I probably would have saved money purchasing the full round trip fare all at once. I bought the return ticket from the Shinkansen office in Kyoto Station, and it was just as easy.
If you are taking a bullet train to or from Tokyo, consider taking the train to Shinagawa Station instead of Tokyo Station. I left for Kyoto from Shinagawa, because the JR clerk told me that would be much easier to navigate than Tokyo Station. I scoffed a little at this, but after arriving in Tokyo Station from Kyoto, I had to admit she was right. Tokyo Station is a rabbit warren, and when you lose your Shinkansen ticket that you need to access the JR gates, and officials keep asking you which concourse you came through and you have no freaking idea, you may be grateful for the relatively tiny layout of Shinagawa.
Taking the Subway in Japan - Use an IC Card
My first impression of the subway in Tokyo is that it is a subway system on crack. It is both incredibly efficient and incredibly confusing. I can't imagine that being my first introduction to a subway system. Despite the sheer size and complexity, there are ways to easily navigate the system. Access to Google maps was a must, and using a Pasmo or Suica card will make your life so much easier.
In Kyoto I did more walking between neighborhoods and attractions, the subway system there is smaller, and buses were a flat fare, so I found it easy to just purchase tickets as I went. But when I got to Tokyo, I quickly realized that approach would not work, because to get from point A to point B, I would have to take two or even three different subway lines, meaning two different tickets to transfer.
So I bought a Pasmo, or IC card from a machine and loaded it up with Yen. This meant I could just tap the card to enter the subway and to transfer between lines, no need to calculate my fair or stop to buy the appropriate ticket. A Suica card is similar, and both can be used on both JR lines and the other private subway and train lines, as well as the Tokyo monorail. IC cards can't be used to access the Shinkansen platforms, but once you are in a city, you can use them. So if I had purchased a Pasmo card in Kyoto, once I got to Tokyo I could have used it.
Getting to and from Tokyo Airports
Narita Express
I landed at Narita International Airport, and had to get myself from there to Shinagawa station to catch my Shinkansen to Kyoto. Narita is far outside of Tokyo (think going to JFK from NYC, but multiply both traffic and distance), so a taxi isn't usually the most efficient option. The easiest option is the Narita Express, a dedicated train line that operates between Narita terminals and a few stations in Tokyo, including Shinagawa and Tokyo station. You can purchase tickets at machines or at the JR East Travel Office in the lower level of Narita. Seats are assigned and there was plenty of space for luggage storage. It takes about an hour to get to Tokyo, and the Express only runs about every half hour, so you do need to budget time accordingly for that. Depending on when you land and how quickly you clear customs, you could be waiting a while for the next express.
Tokyo Monorail to Haneda
If you are flying in or out of Haneda Airport, then the Tokyo monorail is an excellent option for airport travel. I flew home from Haneda, and from my hotel, it was a short trip to the monorail station, and the monorail only took about 20 minutes to arrive at the international terminal. You can use your Pasmo card (or JR pass) on the monorail, and overall the experience was much quicker and more efficient than the Narita express, though this is also because Haneda is much closer to Tokyo than Narita.
The only advice about the monorail is that the platform is on the third level of the station, and from what I could tell there were no escalators, only one elevator. So either wait in line for the elevator, or be prepared to haul your suitcase up three flights of stairs.
If you are getting on the monorail at Hamamatsucho Station, follow the signs for the monorail, then turn to the right out of the station exit. The monorail platform is down at the end of the covered walkway, not straight ahead of the station exit as you might assume from the signs.
Pocket WiFi for Travel in Japan
Literally every guide you read will tell you to get a pocket wifi for your trip to Japan. I know we are all getting text neck, but that's a small price to pay if you want full mobility in Tokyo. I read somewhere that there are no wrong turns in Japan, only new directions, but seriously, a portable wifi is not optional if you want to be able to navigate the city and the train system and you don't have an international data plan.
There are many providers of pocket wifis at comparable price points, but I decided on Ninja wifi, because they allowed for a more last minute purchase where others seemed to require the reservation to be made a 4-5 days ahead of time. I purchased two days before leaving for Tokyo, and just went to the Ninja wifi counter in the arrivals hall at Narita to pick it up. When I flew out of Haneda, I dropped of the wifi at the counter in the departures level.
Carry a portable charger or be careful with battery life, since it does drain the battery to be constantly refreshing maps. On the other hand, battery conservation was a good reason to just put my phone down and observe.
Paying in Japan
Japan is a heavily cash-based society. Most hotels and some restaurants took credit cards, but for the most part, you will need cash. This is somewhat annoying as only large amounts of Yen are in bills, and most of what you will be using day to day, like 500 Yen or 100 Yen amounts, are all in coins. Make sure you have a coin purse or wallet where you can stash a lot of coins, and just be ready to sift through the pile when it's time to pay.
Other Tips for Travel in Japan
When dining out, I found it to be a mix of paying the bill at the table and paying at a counter. I just watched what other people did and copied them.
Most restaurants have little baskets or bags next to the table or under the bar, where you can stash coats and bags while you eat. As a woman who is constantly exasperated when bars don't have bag hooks underneath, I loved this.
There are very few public trash bins in Japan. You can find them at train stations and possibly in convenience stores, but for the most part, you won't see them. You can just take trash back to the vendor you purchased from, or carry it around in a small bag until you find a bin. Needless to say, don't toss trash in a vendor's bins that you did not purchase from them.
