I've already got accomodations lined up, but I appreciate the suggestion!

From what I've heard, I'll be trying to stay as far away from Roppongi as possible...

My Japanese teacher gave me a map of Narita she had from one of her trips back to visit family, and pointed out the important places - where to exchange money, the ATMs, and the JR counter to exchange my pass.

Thanks for the help!

Don't blow your nose in public. Try and bring a pair of slippers. And be prepared for the toilet seats.

That depends on your idea of a good time. I lived in Tokyo during my teens -- went to an int'l high school there -- and still visit often as my parents still live there. Roppongi, if you just like poking around and seeing stuff, is perfectly harmless for a 16-year-old and offers a lot of good photo ops. It is also a "gaijin ghetto" as the U.S. Embassy and residential compound are just a few blocks away so there are lots of foreigners around in the evenings.

Where else in Japan are you going?

Also, don't forget to have your "back story" ready if the immigration or customs guy/gal asks you why a 16-year old is coming to Japan by himself. Do you know anybody in Japan? Have that info ready, in case you need it. Otherwise, find somebody you "know" in Japan before you go.

You may take note of tokyotraveler's excellent adventure. I'm not suggesting that will be you, but (a) lots of good info there, and (b) a cautionary note for the unprepared.

Lastly, do visit the Tokyo forum in FT. It is more about all of Japan, and you'll learn very important facts, like how a SL600 V12 AMG with black tinted windows, 19" wheels, antennas from the back, an Inagawa "super tiger" sticker in the back, and low number license plates will never be stopped by the police when speeding.

Seriously I think the biggest rookie mistake of all travelers is OVERPACKING. I walked into my friend's house and it appeared that he was packing his entire house. He was planning to bring 3 full sized luggage for a 2 week vacation. I helped him narrow that down to 1 bag and only had him overpack socks and medicine. Since Japan is a industrialized nation they do have pretty much have everything as in the US. If you are more of a tourist, I'd also pack a small (empty) duffel for gifts or souviners. There isn't anything worse than buying a bunch of stuff and having to leave it when you realize you don't have space...(as what happened to another buddy 2 weeks ago)

I do have a couple friends I know who are in Japan (other foreigners) and I will probably be staying with my Japanese teacher's family for a few nights. I think being able to talk to the immigration people in Japanese will also help with that issue - it substantiates my reason for coming (because I am interested in and have been studying Japanese culture).

I wasn't going to bring an empty duffel since I was planning on bringing back more than would fit. Instead, I was just going to send my goodies back via mail.

I never pack much, so that won't be a problem

If you've been studying Japanese for a while you probably think you know what's coming. Being in the same situation myself a long time ago, I can assure you that reality will look quite different from your preconceptions, in all sorts of weird but wonderful ways

Do you have somebody meeting you in Tokyo? Getting around can be a little overwhelming for the first time visitor, especially if severely jetlagged and dragging around suitcases, so you might wish to post your first night's destination -- some enterprising FTer will be sure to map out the optimal route down to where to stand on the train platform.

Last but not least, two links:
http://www.flyertalk.com/forum/forumdisplay.php?f=509
http://wikitravel.org/en/Japan

It's good that your Japanese teacher showed you an ATM to get money. With any luck, it will actually work with your banking network. Most of the Post Office ATMs work. However, in my experience (and lots of others who have visited), cash isn't easy to come by, and not all places take credit cards. There's no such thing as checks in Japan...it's a cash country. While at the airport you should probably get enough cash for about half your stay. I know you'll be there for a long time, and I would also hate to carry around that much cash. However, you may not get a chance to withdraw money often, since it sounds like you'll be moving around.

Traveler's checks are another great way to go. Most Japanese banks prefer exchanging those to foreign cash anyway, and they're safer if they get stolen. Just make sure you have your passport when you try to use them, because they'll probably ask for picture ID.

Oh, and welcome to Flyertalk. Have a great trip!

Hold it right there. I would not speak to the immigration and customs people in Japanese, unprompted, unless they ask you if you speak it. Then you can say "a little", or whatever in a sheepish, aw-shucks kind of way, and right away tell them why you speak it.

Letting them know that you speak Japanese but don't live in Japan is an invitation to the proctologist desk in the backroom. They are highly suspicious of foreigners who speak Japanese but don't live there. They find it hard to comprehend that somebody speaks Japanese but has never lived in Japan. They will assume that you are lying and that you are living in Japan on a tourist visa. A blank passport (like yours) is not going to appease them. It may actually arouse even further suspicions given that you may have "lost" or "misplaced" your other passport with your previous entries.

Also, I don't know how much you have studied Japanese, so I can't comment on your level of fluency, but my guess if your studies have been of less than 2-3 years of fairly intensive or immersive Japanese, you are probably not able to hold a meaningful conversation with the immigration officers besides "I like Japan, I have studied Japanese for x months/years, and I want to be a tourist in your country".

I wasn't going to speak it unless they asked - I'm really not confident enough yet, since I haven't ever talked to more than a few Japanese people before.

I just figured that, if they asked, it would help to substantiate my reason for coming.

Sightseeing and tourism are good reasons, too.

I've been to Japan twice, once in 2000 after studying the language and culture for a few years in college, and again this past March. Its a blast, you'll love it!

Seems like you have most things covered, my only real advice is to make sure you pack light if you are using the shinkansen (bullet train). If your luggage is carry-on size or only a bit bigger than that it will make travelling much much easier.

Where are you going besides Tokyo? And when?

I have been in Japan 3 times, all in the last year. I had a lot of fun on all of my trips, especially doing things with native friends that share the same interests. The Tokyo board here was immensely helpful in providing ideas on what to do. Another good resource is http://www.japan-guide.com .