I think your belief that John M. is William's father is fairly solid. On the IGI entry that you referenced he, William, even has a son John M. (named after his grandfather). William and Emily are on the 1880 census in Dover with two of the children mentioned in the IGI entry. On the 1850 census William is listed in the house of his father John M. who owns a farm worth $30,000. They must have been fairly well to do as nobody in the neighborhood owns property worth more than $2,500. I feel certain the middle initial "B" in the IGI is an error. He's shown as William S. on the 1850 and the 1860 censuses, and with no initial on the 1880.