Sabotaging the clock is actually a somewhat simple task- just put the cogs in the same general location. The bottom cog, for example, stays on the bottom but put it on the left side.
Once this is done head upstairs to the next level and pass Dean the cogs you will find there using Wingardium Leviosa. When all three are pased down head back down to place them. Use the pegs that run in a straight line in the bottom right corner. Place them with the biggest cog in the middle and the clock should be nicely broke.