I think that must be difficult for a child to move to a completely new country with a different language in the second grade. I think an important thing to start of with would be to ask the parents to let the child bring some things from home that make him feel comforted or as if he's back in Japan (ex. stuffed animal, pictures of friends/family members, etc.) It is also important for you as the teacher to try to learn some of his language. It might be fun if one day you take time to go over with the entire class words in Japanese that may be useful for everyone to know. You can also correlate those Japanese words with the English equivalent, so not only are the other students learning but your new student as well. In order to put the new student at ease, you can create signs in your classroom with both Japanese and English writing to help him familiarize him with everyday things. Another important step in helping him stop crying would be to assign a few students to befriend him and make him feel comforted so he has someone just there for him, since you as a teacher can't only cater to him.