Hi Pete
One of the biggest problems I found teaching in Japan was the cultural difference of the students. One aspect of this was that in Japan it is not \"done\" to be incorrect in the class, and students get very embarrassed if they are wrong. This means it can be difficult to get them to speak unless they're very sure of the answer or of not making a mistake. This makes conversation activities and even simple things like getting feedback from a grammar exercise quite difficult sometimes.
In terms of grammar, use of articles was one of the bigest problems. I know students from many different language backgrounds have problems with articles, but I found it a particular problem for Japanese students. (There's no equivalent in Japanese).
I think these are a couple of the biggest problem areas. I found a pretty good article about the problem with articles here:
http://www2.gol.com/users/norris/a-the.html
Hope this helps Pete and good luck in Japan, it's a fantastic country to live.