The idiom clean one’s clock seems to have originally been a piece of US railroad jargon, meaning “bring the train to a sudden stop” – i.e. by applying the airbrakes, thus “cleaning” (resetting) the train’s air gauge (clock).
I think the railroad idiom was “clean the clock,” referring to the sudden braking and the resetting of the gauges. The earliest use of “clean <a person’s> clock” is in 1908 and seems to have evolved separately, with a round face being like a clock. Around the same time “Fix <a person’s> clock” meant roughly the same thing–to defeat them thoroughly.
