Matt,
I would guess most of the holes on the second course would have been templates too. If you look closely at the Par 3's on each course, you will notice some of the template holes.
It looks like all the Par 3's were shifted around to me?
The second course never came to fruition because of a conflict with the schools endowment campaign. The cost to construct the first course was more expensive than the golf committee planned for. They started a membership drive that turned out to be very successful.
According to
Golf At Yale:
"Success of the patron program could have financed the full thirty-six hole plan. Unfortunately the committee plans ran afoul of the University, which was beginning its own endowment campaign and feared the simultaneous competition. As a result, it absorbed all of the construction costs into its general budget, but this is likely the reason why the second eighteen hole course was never begun."
Bret