How to change custody status when one parent has moved out of US to non-reciprocating country?

You need to have a good divorce lawyer file a motion to enfoce the judgment and to modify custody, based on the change of circumstances based on your ex-husband's relocation.

You're quite right to be concerned about the fact that Japan has not signed the Hague Convention on international enforcement of parental rights.  While it's a problem encountered more often in connection with Middle Eastern countries, where the law is very different and very seriously anti-womens'-rights, you have to consider the risk, based on what you know about the man, that he would take your son to Japan and refuse to return him.  Sometimes it is hard to persuade a court of the seriousness of this risk, in the absence of some evidence that this is what's planned;  you'll have the advantage of his having used disobedience to the divorce judgment to try and coerce you, because that shows he can't be trusted to obey the law, or a future court order.