Has a College Football game ever ended 39-4?
Exactly once. On November 2, 1889, Cornell beat Stevens 39-4, and no College Football game before or since has ended that way. When it happened it was a scorigami, the first 39-4 in league history.
That makes 39-4 the 1820th most common final score out of 2,216 that have ever occurred in College Football. One point away, 40-4 has happened never and 39-5 has happened 4 times.