First off, if you are taking a long haul flight, have some aspirin and eye drops on you during the flight. Your brain will probably be melting and eyes burning red long before you arrive.
If you don't belong to some frequent flier program, join a relevant one so you can get flight credit for your trip.
If you are American, you should exchange your dollars for yen in Japan. In the US the exchange rates are terrible. Overall it is far more convenient to use your ATM card in Japan at a 7-11 or Japanese Post Office compared to exchanging cash. There will be a certain fee for using it (check with your bank first) as well as a foreign exchange fee, but often is only a few dollars unless you are doing business with a rip off bank. Having your money in a credit union will often be a lot kinder to your wallet in many ways.
If you do plan to use your ATM card in Japan, make sure the bank knows about it first so they don't don't suspect fraudulent usage and freeze your account. I have heard from many British and Australians that the rate is better in their home countries. You can see the current rates in Japan and decide for yourself.
Note that you can not use 1 or 5 yen coins in vending machines and phones.
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Do NOT just automatically get a rail pass. Know where you plan to go and make sure that you'd save money on a pass first. You could save a lot on a pass - I sure have. But if you donft travel enough or travel too slowly, you could lose a lot on a rail pass too. Use a website like Hyperdia and find out the rail fares, schedules, and transfer info, and double check to see if you'd save money. Or for simple round trips, use this handy calculator. And if you travel very far, it'd probably make more sense to fly. Use a low cost carrier like Jet Star, Peach, or Vanilla Air. ANA also has its Experience Japan Fare. These days you can fly across the country for peanuts, and not murder a whole day sitting on trains. If you travel slowly, a series of regional passes might make more sense. Or if very far, a cheap flight plus a regional pass can save time, which matters too, some another tips:
https://exploringthisrock.com/.
For visiting some places like near Mt Fuji or Koyasan, a JR Pass will not help much. But there are other regional passes that may help you. Many people go to see Tokyo and then Kansai (Osaka/Kyoto/Nara/Kobe) for a week. But the Japanican discount ticket is actually cheaper than the JR Pass, you can take the fastest bullet train Nozomi, and get one free day of local transport.
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Do your research. Nothing is worse than wasting time - plan your trip carefully. Know where you plan to go, how long it will take to get there, etc. Carry paper or digital maps of your destinations. Use Hyperdia to know the train schedules. Don't slap your head after your trip because you just found a place you wish you had visited. There are several comprehensive sites you can look through, such as Japan Guide or the JNTO. Many official city and town webpages have their own sightseeing info on them in English, Korean and Chinese, and often you'll find good places that are listed nowhere else.
