It does seem more likely that the grandfather clock came as part of the set design ... if it is mentioned in "Shadows on the Wall," I don't think it's given any significance, just part of the set description, though I don't really remember anything about how the set may have been described. But you're right, the clock really does figure in the story - often just to let us know that it's midnight or early morning hours and people are still up at Collinwood ... or sometimes the clock gives us a countdown to some plot situation, like the Barnabas/Forbes showdown, if I remember correctly. It's interesting that clocks often have some symbolic significance in stories by Poe, thinking of "The Masque of the Red Death," for example.