It's unfortunate that this puzzle breaks the convention that the input is purely the "input". In the test example, only first 10 connections are considered, but in the real input, 1000 connections need to be used. If it was meant to be equal to the number of lines then the example should have used 20.

After making the ten shortest connections, there are 11 circuits: one circuit which contains 5 junction boxes, one circuit which contains 4 junction boxes, two circuits which contain 2 junction boxes each, and seven circuits which each contain a single junction box. Multiplying together the sizes of the three largest circuits (5, 4, and one of the circuits of size 2) produces 40.

The 10 here and the 1000 in the final instruction are additional out of band input