They had been shot in what police believe was a murder-suicide, said Cpl. John Ford.
Police released no details other than the victims' names, ages and address.
Relatives of Shockey said that until recently she had shared the house with Bernard McAfee, who found the bodies. They said Stouffer lived in nearby Maryland, although police listed his address as the Mentzer Gap Road house.
Police arrived at the scene with guns drawn and surrounded the house, neighbors said.
"They told me to go inside my trailer and lock my door," said Sandy Dale, 30, who lives across the street.
Dean Hebb, Shockey's grandfather and owner of Buchanan Auto Park, a used car dealership at 11194 Buchanan Trail East in Waynesboro, said Shockey and Stouffer worked at his dealership, she as a secretary and he in the detail shop. He said McAfee works in the dealership's maintenance department.
Shockey and McAfee lived together in the Mentzer Gap Road home for more than a year, Hebb said. Shockey left McAfee for Stouffer about a month ago, her grandfather said. Over the weekend, she apparently decided to leave Stouffer and go back with McAfee, he said.
McAfee found the bodies after he became worried when Shockey failed to turn up for work Monday, said Tom Miller, parts manager at the dealership and Shockey's uncle.
"He called the house and there was no answer. He said he was going over there to check on Shannon," Miller said.
McAfee (photo: McAfee, left; Tom Miller, uncle, right), who was visibly upset, stayed at the scene for most of the day.
Kimberly Mohn, who said she was a friend of both Shockey and McAfee, said the two were engaged to be married more than a year ago, but that Shockey had left McAfee for Stouffer.
Mike Miller, who was Shockey's father, Hebb, and other relatives stood across the street from the house while police conducted interviews.
Yellow police tape was strung around the two-family residence.
The house is owned by Paul Gunder, who lives next door.
Jeffrey R. Conner, chief deputy coroner for Franklin County, arrived around noon. The bodies were removed from the house after 4 p.m. and taken to the morgue at Chambersburg Hospital. They were to be taken to Lehigh Valley Medical Center in Allentown, Pa., for autopsies this morning, Conner said.
Police said no further details would be released until the autopsies are complete. Conner said the results should be available this afternoon.
Relatives said both victims were shot with a handgun.
At one point during the day, police checked the contents of three vehicles parked at the side of the house, including pickup trucks owned by Stouffer and McAfee and a small red compact car relatives said belonged to Shockey.
Police removed the yellow tape from around the house at 4:30 p.m. and left the scene.