I do not know where you come from, but I hope I can help you. I have some general things to say that might be useful.
I totally understand your state of mind. I did not have much time to prepare to move to Tokyo; however, I lived in a major city in the USA, so moving to Tokyo, in principle, wasn't too much of a big deal for me, because big metropolitan areas do share common traits.
Since I have been here, I have found that to be true. I arrived in Tokyo in August, and I couldn't speak a work of Japanese, and really I can't say more than few phrases now. I came here because I had a job, but I didn't have a place to live. I was fortunate in that a colleague helped me to find a good place to live; I wasn't picky and found what I wanted in one day.
Many things I can offer in a hope to calm you...my situation is that I have a research position at the University, so I didn't come here a cultural exchange program. This does not mean that I am not interested in learning about Japanese culture, it's just that my employers expect me to be working full time.
You are going to have some 'up's' and 'down's'. In the first month here, I had a lot of 'down's.' A big deal for me was to find a place to live where I can walk to my work, so if I am not doing so well, I can always walk home in a few minutes and then get back to work without missing so much time. You might want to think about living close to your work.
The trains/subway will seem intimidating; it's not, you'll find it easy to get around after a few trips. It is really crowded at times, as Joe already said in his post.
Patience: Just be prepared to take longer to do stuff than you normally would. Walk around your neighborhood a lot and get a feel for the shops there. Visit all the markets to see what they offer. If you are travelling somewhere by train/subway, leave early, so you can take your time. It will be easier on you, stress wise.
Communication: I actually have not had a problem communicating with anyone. In my experience, it seems that the Japanese understand English very well; they actually speak it well too, but they do not think so and will be reluctant to speak in English. With patience, and a lot of 'please' and 'thank you', you will not have a problem communicating.
Bank: Try to find a colleague to help you open an bank account. There is a **lot** of paperwork in this city, and getting a bank account isn't something you will want to do on your own.
At my job, there wasn't anyone in charge of acclimating the foreigner.
My new Japanese colleagues were helpful, a lot, they helped me find a place to live, buy a futon to sleep on, and got me started with the trains/subway. But there's going to be a point where you have to do stuff on your own. This web site, for me, has been extremely useful. There is a ton of information here.
So, don't panic!
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