I typed this up for a friend.
A couple of things about a trip to Japan:
a. Japan Railway Pass
In the past I bought this twice and I used JTB USA (New York Branch)
You need to buy this before your travel to Japan (You can't buy when you get there). When you arrive and go to the JR station (Japan Railway station) they will stamp your pass. I don't buy this anymore lately just because my hometown now has a local airport and I just fly directly to that without taking the train.
b. Yen - Dollar exchange
I usually buy yen from a local Japanese resident in DC area by going to the local website.
I usually say I need Japanese yen and propose to use the exchange rate of that morning when I got meet the person. I am not super sure if this saves money. Last time I calculated and compared with the exchange rate they use at Narita International airport, the difference was not that great. But I like the feeling that I already have Japanese money before I leave the US.
c. Flying in and out
Narita is the international airtport, but I notice that recently Haneda is also a possibility. Haneda is in Tokyo, so if you have a choice I recommend using Haneda. Narita is like an hour or so away from Tokyo.
d. I think you can also arrange such that you fly into Tokyo but leave from another city in Japan like Osaka. That way, you can make your trip efficient.
e. A lot of people go to Tokyo and then Kyoto, Osaka, and Hiroshima.