Japan is not America. There are a lot of similarities and the daily life vaguely resembles Western life but there are some minor and some major differences. People here do not generally speak English. While a lot of signs include English - the amount people speak is very limited. Granted, they speak more English than Americans speak Japanese. One helpful thing is that a lot of words are borrowed from English so if you pronounce certain things with more vowel sounds and change L's to R's, you might be able to get your point across. Less is always more - if you can ask in Japanese, use as few words as possible because the more words you use, the more likely you are to confuse people. I know this is an over-blown generalization now but the shoe fits...being louder doesn't make people understand any better. Imagine if I yelled, "Doko eki ni desuka?" at you...chances are I could yell this until I was hoarse and you'd have no idea that I asked where the train station is.
You will definitely know when you have to take your shoes off. This is necessary when entering a home and there are a few places of business (schools, restaurants) that ask you to remove your shoes. You'll see steps or shelves with a bunch of shoes. I've never been caught off guard so I don't think it's that tough.
In the train station, you buy tickets from little machines. I think most of them have an English language setting. Once you buy the ticket, you take it to the gate and put it in the machine and walk through and grab the ticket on the other side. If you wait too long, the ticket will get sucked back into the machine and you'll have to talk to someone and who knows how that will end up. Once you've arrived at your destination you put the ticket in the machine again and this time the machine takes the ticket and you're done. If you've done something wrong, little doors will close and you have to try communicating with the train station workers. Overall, it's pretty intuitive but some people have issues. People wait lines by arrows for the trains because that's where they stop and people (de)board.
On the train, you shouldn't talk on your phone. It won't matter much because people visiting won't have them but people don't talk on their phones on trains. Also, if the train is any bit crowded and you have a backpack, take it off and place it between your legs to make more room.
Most places are cash-only. Some places take credit cards - department stores, American shops but generally everything is cash-based.
There is no tipping in Japan. It's mainly because they are being paid for their work. That's a point of pride and tipping is considered somewhat rude - this includes waiters, taxi drivers, barbers, etc.
In restaurants most people drink water. Usually it comes in very small glasses. You can always ask for refills or some places give you a pitcher. Soft drinks are available but they are expensive and there are no free refills - same goes with coffee (except Mister Donut). The portions are smaller than you think. If you want to eat traditional Japanese foods - you should learn to love noodles and rice. Generally the food is not very salty and, therefore, may taste a little bland to you. Not everything is sushi - as a matter of fact, it's not as pervasive as you'd think. It's definitely more accepted here as normal than America but it's not everywhere...I have a good number of students who don't like fish - that shocked me. They do ALL eat rice and miso soup.
Drinking alcohol in public is perfectly acceptable. But a caveat to that is that drinking anything while walking or wandering around stores or whatever is considered rude. People do it but it's frowned upon and you may get dirty looks. It's the same but a little worse with eating. Usually if you are out of peoples' way and standing still against a wall or something, eating and drinking is fine.
You get a bag for almost everything.
Garbage cans in public are really difficult to find. Normally there garbage cans near grocery stores and convenience stores but I am not sure where else with regularity.
Most people wait for the lights to cross streets. Some people cross but most of the time, there is a gathering of people waiting for lights.
Oh, and there are money trays that you put money onto. Handing money to people kinda takes them off guard.
That's all I can think of right now - I'll try taking some notes while I'm out to see if I can think of other things.
Here are some random pictures: