In retrospect, where are the hints readers have about the plot?

If by plot you mean where the story's action ends up—with the discovery of Homer Barron's skeleton—there are a few key clues that lead up to that surprise ending.
The three clues are the smell coming from Miss Emily's house, the scene in which Miss Emily buys poison, and the mysterious disappearance of Homer Barron. In fact, after the reader learns that Homer's skeleton has been kept in Miss Emily's house for years, it's hard to imagine how we didn't know that's where the story is headed all along. However, the non-chronological order of events and the lack of information on the narrator's part contribute to the shock effect of the story's conclusion.
The smell is mentioned in Part II of the story, and since it's out of context, readers might not associate it with any wrongdoing on Emily's part. People think it's "just a snake or a rat" killed by her servant. The townsfolk feel like they cannot mention the smell to Emily due to her lofty family history, so people try to deal with it on their own. This scene occurs before Homer is even introduced, so we would not connect him with the smell at this point.
The next hint, in Part III, is a bit more obvious, which is when Emily buys poison from the druggist. The scene is clearly suspicious, as Emily does not want to tell him why she's buying the poison. She simply agrees with his suggestion. The druggist says that arsenic is used to kill rats, so Miss Emily says she is buying it "For rats." We get the feeling, though, that it's not why she's getting this poison.
In Part IV, the town thinks Emily will kill herself with the poison, but then more information is given about the history of her relationship with Homer. The townspeople start to think she and Homer will marry, but then again, they are "not surprised when Homer Barron—the streets had been finished some time since—was gone." This is mainly because his job in town is finished, and they think maybe Emily has married him and will go move with him up North. This sudden disappearance, though, is definitely suspicious. Once we learn that Homer's body has been in Emily's home all this time, in a make-shift gothic bridal chamber, and that she has been sleeping next to him recently, all of the clues make sense, and we can see how Faulkner foreshadowed this ending.