Are you just planning on staying in Tokyo, or going elsewhere. Kyoto is only a few hours away by train, and they have some really nice temples there.
Here's some advice from my trip to Japan.
Tokyo
In Tokyo, I mostly just wandered around and saw the city. It’s an amazingly large place and always crowded, but it can be a lot of fun. I was staying in Ginza, which is a high-end shopping district to the south-east of Tokyo train station, but I don’t think it really matters where you stay as all areas are pretty accessible by Tokyo metro.
In a big city, it’s always a good idea to get yourself up high to get a view of the place. The Tokyo Tower (Eiffel tower look-a-like) or Tokyo City View, both close to the Akasaka / Roppongi area both offer views, but both cost money. Instead, head to the Municipal Building to the west of Shinjuku station, where you can get up high and get a view of Tokyo for no cost. If you’re lucky, you might be able to see Mount Fuji, though I never did due to either overcast skies or hazy smog.
Also to the west of Shinjuku is the Shinjuku NS building with it’s amazing 30 story atrium and the Park Hyatt hotel, which is a good place to go for some expensive drinks with a great view. It’s the same hotel featured in Sofia Coppola’s Lost in Translation.
To the east of Shinjuku is some great discount shopping, as well as the red light district and the area called the Golden Gai. The Golden Gai is a number of really small alleys filled with bars that many Japanese hit after work. However, a number of places are private clubs or don’t allow foreigners inside. Those that do allow foreigners usually charge a cover charge and pricey drinks. It’s interesting to see, but may not be a great place to drink every night.
Money
The Japanese use the Yen (¥). There are both notes and coins. Most likely, you’ll see 1000, 5000 and 10000 yen notes. ATMs (see below), mostly give out 10000 yen notes. Coins come in denominations of 500, 100, 50, 10, 5 and 1. All notes and coins are marked with the denomination of the bill or coin with the exception of the 5 Yen coin, which is bronze with a hole in the middle.
ATMs are plentiful, but most are not hooked up to the International networks, meaning that you can’t get money. For international travellers, the best choice is to find an international bank. Citibank was the most common. Also, the postal service has ATMs that are hooked into the international network, though those are only open during the postal office hours. Look for ATMs with English instructions, or ask at the TIC or your hotel where the nearest international ATM is.
Credit cards are not widely used, and even most hotels expect cash payments.
Getting Around
For subways, the price of your ride depends on how far you are going. There will be a map indicating the cost from the current station to all the stations in the system. Carry your city map with you, as it includes an English subway map and could come in handy if the station’s map isn’t in English. When you enter the subway, you put your ticket in the gate and retrieve it. When you exit the subway at your destination, the gate will accept your ticket and keep it. Don’t worry if you didn’t put enough on your ticket. All subway exits will have a place to add additional value to your ticket so you can exit.
There are day passes and stored value cards that could be of value if you are travelling a lot on the subways.
I took the bus in Kyoto and the tram in Hiroshima, and they had a similar system. You purchase a ticket and get on the bus or tram. Upon exiting, you present your ticket at a machine by the driver and exit.
If you want to read some other advice, you can check out my trip report on my blog by following this link.