[NewYorkDoctorD]

1) convience stores are good, with food fresher than you would normally expect, plus if you have poor japanese skills you can survive off them
2) keep your passport on you, bored cops may harass you
3) do not buy brand new shoes and then walk around japan, make sure they are broken in first
4) find a bakery, the quality of the flour used is typically very high, at least compared to the US
5) eat a curry donut, just don't expect to work out right afterwards
6) be polite but firm if someone wants to practice their english with you, you have a pretty aggressive schedule so you will want to make the best of it. Kids on school projects to practice english can be fun though.
7) onsen may or maynot be open in nikko (though your hotel might have outdoor bathing facilities), pick up the bus pass if you intend on goign up into the lake area
8) there are typically no fees for using your atm card at a japanese post office, but your bank fees still apply
9) ramen might be more difficult for you for dietary reasons, but if you do decide to partake, it helps to know the kanji for salt, miso, shoyu etc if you are picking up a ticket from a vending machine
10) men's magazines are porn, women's magazines are typical magazines intended for women
11) a fair number of places will have pictures or wax models of the food, you can always point to what you want
12) walk around with a bottle of water, drink sizes are smaller than what you are used too
13) if you have a student ID, use it often as it will net you considerable savings
14) i assume you are arriving into tokyo. If you are planning on taking the narita express, go to the JR travel office and show them your passport to get the suica/narita express combo
http://www.jreast.co.jp/e/suica-nex/ you will save 1500+ yen depending on the route compared to purchasing a suica card and Y2000, if not take the keisei skyliner as it is waaaaaaaaaay cheaper than the narita express
15) if you have time to kill in tokyo, which you probably wont, spend some time in a tokyu hands
16) if you see a store that says video/books or AV and the character for books, it is a porn shop, not a book shop