This is about tourism and culture, not about how to have a good time ...
The simple guide to having a good holiday in Japan. You should all do it! Well, if you've never travelled anywhere before, I suggest you warm up with a weekend in somewhere where you can't understand the language, like Glasgow - Amsterdam does not count, their English is too good.
1. Buy an air ticket to Japan. Try not to fly Aeroflot or a carrier about to go bust (like Alitalia). ANA are nice.
2. Buy a Japan Rail Pass for however long you are going to be there. Critically this must be done before you go there. When in Japan, use the railpass to reserve seats wherever you think you might be going.
3. Book yourself into an airport hotel for the arrival date, and the day-before-departure date if your flight is early in the morning. For Narita, the Holiday Inn is quite nice and cheap.
4. Book your other accommodations. Stick to "business hotels", they're midrange hotels at cheap prices, near the railway stations or town centres. They have air con, rooms with showers but not enough room to swing a cat, usually hot and cold running Internet. Book a Ryokan or other exotic accommodation if you can find one that speaks English. Make sure they take credit cards.
5. Hunt through the JR East, JNTO, local government, hotel, japan-guide.com, etc, websites. Print off all useful info especially the maps. Print off your hotel name and address, preferably in Roman and Japanese characters. Print off tourist info on places you want to go. Read up on how the rail system works, like at "byun byun shinkansen". Print off subway maps of places you might want to go. Try to find bilingual maps if at all possible because then random Japanese can help you out better.
6. Buy a tourist guide (the Lonely Planet works fine, the "Japan by Rail" guide is more idiosyncratic but more informative (I used both)) and a phrasebook (try to find one less useless than the Lonely Planet one). Try to work out how to pronounce the basic phrases (hint: don't drawl, the syllables are all fairly short).
7. Pack all your clothes, etc. Japan's got drugstores for shower/bath stuff, makeup, etc. It hasn't got many English book shops. Bring a long Ethernet cable or a small wifi router because business hotels usually have internet but often don't have any ethernet cable in the socket for you. Don't forget to bring a camera!
8. Learn what natto looks like.
9. Eat only at restaurants where you've read an English menu or seen a picture or a plastic model of the food you want to eat. Decoding ideographs just takes too long. This limits you to about 90% of Japanese eating places and ensures a natto-free life. It also makes ordering a lot easier all round. This is particularly critical if you are allergic to something or picky (including vegetarian/vegan/etc).
10. Vending machines (for drinks, mainly) are everywhere, so are convenience stores selling essentials like snacks, drinks, beer, and umbrellas.
11. Always hit the tourist info whenever you arrive somewhere new, bearing in mind they tend to close at 19:00 or 20:00. They have bilingual or English maps, transport info, etc, etc. Keep plenty of cash on hand, since most of the cash machines that take foreign cards are in the post offices and they keep similar hours (even for the cash machines!) to the tourist info.
12. Find some stuff to look at or stuff to do. There are so many things to do you won't have time to do them all. Just enjoy what you can.