I think the biggest challenge I found about Japan was constantly being wrong. A week in Tokyo made my hypersensitive to every cultural misstep I made. And, the really crazy thing is, there’s just so many to make.
I like to think that I’m not the most culturally insensitive person out there. I grew up across a number of countries in Africa, Asia, and the West. One of the primary schools I went to had over 80 nationalities represented. There were two Australians there. I’ve spent evenings sitting around a tin drum fire signing with Cuban refugees. And yet, even with all that, I couldn’t for the life of me avoid making cultural mistakes. Even crazier, after I’d read up on as much as I could about Japanese cultural heritage.
There’s so much that makes a lot more sense when you have an appreciation of where the country’s come from. I can’t claim to have a spectacularly deep understanding of what makes Japan tick, but even after having read just a little, so much makes more sense. Karaoke, origami, the Otaku, and the emphasis on etiquette and role-playing - it all makes sense when one understands the contraints the Tokugawa Shogunate imposed. But, that’s for another time. This time is for my Gaijin blunders. 
It was even simple stuff. When we landed after twenty odd hours of being awake, we arrived at the hotel to find out that we couldn’t check in until 3:00pm. While were trying to get ourselves organised, I lay down on my back for five minutes on one of their benches. Next thing I knew, I had the manager tapping me on my shoulder, telling me to sit up. In his context, that was totally appropriate - I was being messy by lying down. And, by doing so, I was bringing embarrassment to his establishment. On the other hand, my own Western context was that the customer’s always right (well, most of the time), especially in hospitality. So, in doing what would be fine elsewhere, I embarrassed him and myself.
We had the same issues getting on the trains. Unbeknownst to us, the signs actually tell you the length of the train, how many carriages are arriving, and even where the doors will be. So, you can line up at the right lines, if you know they exist. Needless to say, we didn’t. Even with Lonely Planet (now there’s one for the books, pun intended). So, we unknowingly cut in line repeatedly for a few days until we clued in.
The worst part is that most people are too polite to tell you you’re doing anything wrong. So, you keep doing them, not because you’re intentionally being rude, but because some of the cultural rule are so subtle as to be almost invisible.
The flip side is that people can be apparently unbeliveably rude without meaning to. Another thing that took us a day or two to work out was that there are rules for lines. There are rules for everything, but that’s neither here nor there. With lines, they apparently go parallel to the counter. So, even when we were standing next in line, people would queue up to our right because we weren’t a step over and forward. For want of a foot, we’d lose our place. And, it kept happening until we realised why people were happily cutting in front of us.
More later.