Here is a good place to start. Most of them are not earth-shattering and make you want to run for the exits. Some things may even become annoying.
http://www.thejapanfaq.com/FAQ-Manners.html
A couple of my own:
Parties or social functions can be set with a stop watch. As soon as its 8 o'clock or whatever every packs up and leaves even if its in full swing.
People do not usually socialise at home so it means having to spend money on restaurants.
Crowded trains.
Long meetings that seem to go around in circles.
Senpai-Kohai. Strict delineation based on seniority age and whether a person comes before you or after you in the company.
You might be a talented guy with great ideas but there will be older people in the company they listen to first.
A lot of times people are not prepared to think outside the box but run around like a bunch of chickens in a cage and stick together.
It takes a long time to make real friends, especially outside the work place, Drinking buddies, , acquaintances co-workers yes. Most I would not consider real friends though.
What people say and what they actually mean can be two different things. There is the public face and what their real thoughts and intentions are. Learn not to take things at face value.
Japanese will tell you what they want you to know, and it is a good idea to learn the difference.
The high cost of living in general.
Lack of public spaces, greenery.
If you look Chinese or Asian you will of course blend in, just like a Caucasian stands out like dog's balls. That doesn't make you any more Japanese though. Japan has an expression. ²Ιόκ²Ι]@which means "when in Roman do as the Romans do". They will appreciate the effort to fit in but it wont make you any more Japanese. Some foreigners tend to go overboard and try and be more Japanese than the Japanese.