I finally got my father's birth certificate (Sokichi Ono, aka Charles Stewart) translated through a man who replied to my original post. He was able to contact my father's cousin whose family were mentioned in the tohon. Email addresses and family photos were exchanged, which confirmed the connection. My husband and I went to Japan to meet the family and we were able to visit the grave in the foreigners' cemetery.
We also found the Akamon temple in Yokohama where the rest of the Ono family are buried and the priest allowed us to visit the grave.
I have not had sight of a census, but James and Take went to live in Kobe after the great Kanto earthquake of 1923 in which their house in Yokohama was lost. My cousin Takahiro Ono still lives in Kobe.
Thank you for your interest - I had a successful outcome and I hope the same will be for you.