1. The railway is EASY - don't stress! Buy a JR Pass before you leave your country if you're planning on taking even one bullet train. It's already paid for itself. Just swan in and out of Japanese railway stations by showing your pass to the man in the booth by the ticket gates. Buy a Pasmo or Suica when you get to the airport or a main train station. It's like an oyster card and works on most urban trains and buses. Tap in and out of the gates. Panicking or lost? No problem. Say your destination station to a man in a booth in your best Japanese accent and they'll invariably tell you the platform and departure time of the train in English.
2. Almost everyone speaks a little bit of English, and anyway all the signs you're going to need are in English as well as Japanese. But it's cool to have a couple of words or phrases in the bag to show willing. My favs are: 'sou-i ma sen' (excuse me), 'ouishi' (delicious) and 'arigato' (thank you).
3. Winter goes well on into March and it's freezing at night time. Don't think you can get away with a Spring jacket. You can't.
5. Avoid the tourist trap temples if you can. Japan is littered with temples and shrines, so just make sure you factor in the 50 foot Buddha in Nara Park, and if you really wanna get stuck in to the religious scene, plan an overnight stay at Koyasan, which is literally a town of Buddhist temples on top of Mount Koya. I stayed at Saizenin.
6. Bridget Jones' mother may have had them pegged as a "very cruel race" but the Japanese are soooooooooooo helpful and soooooooooooo friendly, trust me. Sit down at a sushi bar and look confused and the Japanese businessman to your right, with immaculate English, will not only explain to you what everything is but let you try some of his too. At least that's what happened to me. If you don't much like engaging with other humans and would rather figure out everything on your own, consider investing in a Japanese data sim card, so you can at least use Google maps and translate if need be.
7. The country is one giant restaurant. Eat whenever you can, wherever you can. You won't regret it. The food is basically why I went to Japan, and I wasn't disappointed. Sushi, udon, curry, meat and seafood pancakes, Buddhist vegetarian... it's all delicious.