The more you can prepare yourself for it, the less traumatic the transition will be. Learn as much as possible about the Japanese culture and current events before arriving in Japan. Language lessons, of course, can be particularly helpful. For some useful resources, check our Facebook page: http://www.facebook.com/tokyoorientations/
or Twitter: @tkorientations
A positive frame of mind also helps a great deal when confronting things new and different. Keeping an open mind and a flexible, adventurous attitude will make your adjustment to Japan a lot easier and more enjoyable.