What are three physical clues used in Hounds of Baskerville, not counting the Boot and the letter?

In Sir Arthur Conan Doyle's The Hound of the Baskervilles, Dr. Mortimer recounts the tale of a curse upon his family name. He has a letter dated from 1782 that describes the presence of a "hound of hell," a hound that is much bigger and more terrible than a normal hound, and that has scared many to the literal point of death. 
Dr. Mortimer offers the clue of his eyewitness testimony of the footprints of a gigantic hound. In chapter five, Watson gives an account of the clues collected at that point in the mystery: 

Another item had been added to that constant and apparently purposeless series of small mysteries which had succeeded each other so rapidly. Setting aside the whole grim story of Sir Charles’s death, we had a line of inexplicable incidents all within the limits of two days, which included the receipt of the printed letter, the blackbearded spy in the hansom, the loss of the new brown boot, the loss of the old black boot, and now the return of the new brown boot.

The man in the hansom cab tells the cab driver that his name is Sherlock Holmes. The man turns out to be Stapleton, the man who wanted the Baskerville family home for himself, who acquires the hound and treats it with paint to make it more terrible looking. He stole Henry Baskerville's boots to give his scent to the hound. Another clue Holmes uses to solve the mystery is the scent of the paper in which the warning was given. Holmes smells white-jessamine, which suggests to him that a lady is involved, and points him toward the Stapletons. The sobbing woman is a clue Holmes' uses to link the Stapletons to the crime, as well. There is a subplot that contains the story line of the escaped convict, a light that appears where he is living, hidden by the Barrymores. Another physical clue is the shadowy figure that appears on the moor. The family portrait is what Holmes uses to connect Stapleton to Hugo Baskerville, thus deducing that Stapleton is a relative. 
So in addition to the boots and the letter, there are physical clues of a woman sobbing, the scent on the paper, the light on the moor, the shadowy figure on the moor, and the family portrait.