I have on occasion talked and posted (elsewhere) about the 5 stages of living in Japan. Though this list is fairly subjective, I have seen the progression in people other than myself. When you move to Japan you'll probably go through the following stages:
Green - Wide-eyed amazement, the big screens in Shibuya, the toys, the people, the clean and punctual trains.
LeafGreen - Honeymoon. You've just moved here, life is good and exciting. You're learning new things every day.
Orange - Culture shock creeps in. "What do you mean I can't order extra mayonnaise?" "How many times do I have to fill out the same form??"
Red - Aggression. The trains are too crowded. Salarymen stink. People are not friendly at all, just very annoying and unaware of others. No one speaks English one tiny bit after 6 years of mandatory study at school. Some things are way too expensive. Tokyo is dirty. Mental isolation. Pure hatred! Rampant racism and xeno-ignorance.
Grey - Acceptance. Hey, Japan is a country pretty much like every other country in the world. It has good points, bad points, nice people and arseholes. Live with it.
Now the speed at which someone moves through these stages varies from person to person, obviously. And it isn't always linear. After more than 5 years I can still slip back to the red phase occasionally. On holidays or when I go somewhere nice with the wife it can still feel very much like the leafgreen phase. Generally, though, I'm fairly solidly in the grey phase, but it took me a few years to get there.
My only advice is to grit your teeth when you get to the red phase. Usually people get through it, but at this point the temptation to just give up and move back home can be very strong. But also keep in mind that maybe, just maybe, Japan isn't for you. If you're in the red for a long time you may have to consider the possibility Japan isn't going to offer you what you thought you'd get out of it. And there is no shame in that.