A loon, in this context, was just the youngest member of the farmtoun's "crew" (complement of workers) who got all the most menial jobs; "Syne I got on for third" means he later got promoted to "third man", in which position he'd be in charge of a pair of horses.  A useful book to refer to here would be The Ballad and the Plough (David Kerr Cameron, 1978).

Malcolm