The Japanese have a lot of respect to their food. They are so passionate about it and think that doing anything else (except talking) during eating time is wrong. The theory, so I understand, is that the food is made for enjoying it to its fullest, so doing ohterwise would not bring the joy that foods supposed to bring. Anyone correct me if I'm wrong on this one, but this is what I understand.
And, don't worry about it. I know the Japanese, at least the older generations, think it is rude, but I do it and many other Japanese do it too, so don't sweat it much.
Just behave like you would in your home country and with some common sense and everything will be alright.
Oh, and garbage bins are so difficult to find. There are not public trash cans. Only ones in commerces, like in front of a vending machine.
Mauricio