I worked in a software company in Japan 3 years ago. Fortunately, the nature of my work involves my spending the bulk of the day operating all alone and away from both the company and coworkers. Unfortunately, that means I'm very limited in what sort of advice or consolation I can offer you.  I'm sure you should know this by now, but nomikai (drinks after work) are good way to bond with co-workers in Japan.

How you cope with Japanese way of working depends on you as well. I think you'll do great, one of the hardest things to do is first confront a problem, right or wrong, particularly here, you will learn from this experience and it will make you more ready to face the next one that comes up. Good luck!

I was transferred to Japan for off-shore project and during that time I learned enough to read technical material, conduct business correspondence and had no problem reading and following the instructions or opening a discussion with my co-workers.