Hi magnoliasail and welcome aboard.
I and Thomas have posted abit about making contact with public offices and such in Japan in other threads. In this same People search category.
You first best bet would probably be to start with a Japanese consulate/embassy that's close to you and ask them how to get family registrar information and such.
I haven't posted this information yet, becuase I totally didn't think of it, but Japan does have Private Investigators. They're normally used to check up on unfaithful husbands but I'm pretty sure that some might speak a bit of English, err enough to realize who you want to find and such.
good luck