The hand of the clock determines where in the code the number should go. Start from the earliest time, and place the respective number in each slot.
Oh trust me I agree, I only figured this one out by looking into the files to be honest.
I think maybe changing up that puzzle would be for the best, everyone I have sent the game to has gotten stuck there.
I think changing the numbers up would be enough to make the puzzle more clear. The fact that it's 1-5 throws off everyone who sees it. Throwing in a 7 or a 9 or something would do wonders to make it clear those don't represent the place in the code.