It's on time, and it works
Things run smoothly in Japan.
Good to Know
Use Google maps to navigate your way around the cities, track down 7eleven stores, locate restaurants, keep track of when the next Yamanote line train departs for Shibuya and a bazillion other things. And you'll want to keep track of those subway exit numbers (they're on Google Maps if you zoom in enough), they make life so much easier. Oh, and if you don't do roaming, be sure to get a pocket wifi thingy.
Stand to the left when riding escalators. This goes for pretty much all of Japan with the exception of Osaka and a few other places.
Credit cards are less likely to be accepted the further you get from the major cities. And it's sometimes hard to find ATMs accepting foreign credit cards, so you'll want to plan your cash logistics accordingly. Your best bet are the ATMs in either 7eleven or, as of recently, Family Mart convenience stores. Citibank ATMs usually work well too.
When communicating, the Japanese use ✕ for no (indicate with your index fingers crossed) and ◯ for yes (indicate using 👌). This along with the insane politeness of most Japanese people will get you a very long way when trying to bridge those language barriers.
Taxis are absolutely everywhere in urban areas and they're all safe and easy to use. To compensate for language difficulties, have the appropriate map and/or address ready on your smartphone.
In elevators, the open/close doors buttons are typically operated by the first person entering the elevator for the duration of his/her journey. You won't need to do this, though, so no worries, but it might be interesting to know...
Get an Suica card from a public transport ticket machine. It's a sweet thing enabling you to blip your way through public transport, pay for stuff at a convenience stores or purchase a drink or two from (many of) those omnipresent vending machnies. These cards work throughout Japan and here's how to get one.
Have cash at hand since you may very well find yourself in a situation where it's the only way to do what you need to do. If you're about to venture far out into the countryside, be sure to load up with a bit of cash before you go.
Shiroyama Kanko, Kagoshima
Want to get a bit of a feeling going for what Japan is like? This collection should get you started