Dunno about the origins of the use of Junior, but certainly the British Public Schools had a 'minor' (followed by Tertius? and Quartus?) to show younger brothers who were going through the same school as their elders. See, in The Complete Stalky & Co (Rudyard Kipling), the story with Mr Browning, Uncle Remus and Minor and Tertius running on the sands before 'Pot' Mullins' ash... (Wish I could remember the title of the story. It'll come to me.)