Has a College Football game ever ended 49-43?
Exactly once. On September 27, 2014, Yale beat Army 49-43, and no College Football game before or since has ended that way. When it happened it was a scorigami, the first 49-43 in league history.
That makes 49-43 the 1819th most common final score out of 2,215 that have ever occurred in College Football. One point away, 50-43 has happened 6 times and 49-44 has happened 3 times.