1. Go to a travel agency to pick up some brochures about Japan.
2. Decide which cities you would like to travel to within your allotted time.
3. Make an itinerary of the attractions in those cities.
4. Decide which airline you would like to use and purchase a flight ticket from them.
5. Make reservations and pay for them BEFORE you depart for Japan(Do not wait until you arrive
in Japan to make reservations).
To get a feel for the real Japan, plan on staying at least one night in a Ryokan(Japanese Inn).
6. Purchase an exchange voucher for a 14-day Japan Railpass at an authorised travel agency near you. Then you take this voucher with you and exchange it for the real pass upon arrival at any Midori-No-Madoguchi ticket office or Tourist Centre at train stations and major airports.
NOTE: 'BELIE' is giving you INCORRECT information about the JR Railpass. It does NOT have to start from the day that you arrive, nor does it have to be a week. In fact, you can specify on which day you wish the pass to start, and on which day you want it to expire(You could start it mid-week if you wanted to).
Even the example she gives is INCORRECT. The JR Railpass is valid fo UNLIMITED rides on the NE'X from Narita to Tokyo(including return trip), all JR local trains and buses(except if they travel over a toll highway), all Shinkansen(bullet trains), except the NOZOMI, as well as the JR ferry to Miyajima. It is also free to make a seat reservation in advance(recommended).
The JR Railpass WILL cover you for your return trip to Tokyo(as many as you want in fact.)
It takes only about three hours from Tokyo to Kyoto, so in one day(12 hours) you could make 4 trips(incl. 2 returns).
Most sightseeing places in Tokyo can be reached via the Yamanote Line, for which your railpass is valid, and thus, do not require additional fees.
Night buses are much slower, thereby reducing your amount of sightseeing time, and their routes are also limited. I don't recommend using them.
In Kyoto it is worth it to buy a 1-day buspass for 500 yen.
7. Exchange enough money at a money kiosk so you will have about 20,000 yen upon arrival in
Japan(Do NOT wait until you are in Japan to exchange your money, and also do NOT get yen
from your bank otherwise you will get hit by severe exchange commisions).
8.Bring as little as possible, and do NOT bring a large suitcase. Although there are lockers at many train stations, they are far too small to accommodate a regular suitcase. My regular-size backpack on wheels does not fit in the smallest locker. Do bring a currency converter to instantly know how much you will be paying for items.
Renting a cellphone is expensive in Japan. An international phone will not work on Japanese phone systems. No need to rent a phone if you don't plan on calling your native Japanese friends. Better to purchase a prepaid phone card and use them in regular landline pay phones.
WHAT TO DO IN JAPAN:
As to what to see and do there, this depends entirely on how long you will be in Japan, where you will travel to and your interests.
Things to see and do in random order all across Japan:
Tokyo:
Tsukiji (famous fish market)
Meiji Jingu (old shrine)
Kaminarimon (old shrine)
Asakusa shopping arcade.
Tokyo Tower.
Ginza shopping district.
Sumo wrestling in Ryogukan.
Watch a Kabuki theatre play at Kabuki-za in Ginza.
Oedo Onsen on Odaiba(hotspring bath and sandbath on manmade island.
Take a tour of the Sumida River in an original Yakatabune.
Kyoto:
Gion district{chance to meet real Maiko-san(geisha)}
San-Juu-San-Gen-Do(huge collection of wooden painted buddhas)
Heian Jingu
Kyoto Tower
Ginkakuji(very old temple)
Kinkakuji
On Shikoku Island:
Shikoku museum of private houses
Dogo Onsen
Nikko:
Toshogu shrine
Nagoya:
Nagoya-jo(castle)
Nagoya television tower.
Nara:
Todaiji(huge buddha)
Ushiku, Ibaraki
Amida Daibutsu(largest buddha in the world, which is entered in the Guinness Book of World Records)
Osaka:
Osaka-jo(castle)
Himeji:
Himeiji-jo(castle)
Kumamoto:
Kumamoto-jo(castle)
Near Nagasaki:
Huis Ten Bos(huge theme park)
Okinawa island(gorgeous beaches and sea) and
Shuri-jo(castle)
Miyakojima
With exception of the Yakatabune cruise in Tokyo I don't recommend going on any tour since most of these do not pick up or drop off at your hotel, and many are 'self-guided', and do not have an English-speaking guide(JTB and HATA are two such companies.