Jim,
From reading the old Taft Papyrus newspapers, it looks like the older 9, that still exists today, was added in 1931. I still can not tie a name to that nine holes. According to the Taft Papyrus, there were only a few alterations made to the course in 1915, and that was to the original course that was laid out in 1898 by the President of the golf club, Harley Fish Roberts. In 1900, they brought in an expert, employed by New Haven Golf Club to redesign Harley's layout. (Was this Robert D. Pryde)?
It looks like Horace Taft was part of the golf committee that got the ball rolling along with headmaster Harley Roberts, but the papers rarely mentioned William H. Taft. Horace Taft won the first golf tournament ever hosted by Watertown with a score of 99!
In an issue between 1900 and 1902, they mentioned that the faculty of Hotchkiss challenged the faculty of Taft to a golf match. There never was a follow-up story.