The 37-year-old loner was said by neighbours in Livingston, near Edinburgh, to fit the description of a man police wanted to trace in connection with the case. He is believed to have hanged himself.
Harris had failed to appear for a court hearing on 22 August, the day after Rory's body was found and four days after Rory went missing. A warrant had been issued for his arrest.
"If it was him who killed that little boy we will all sleep better at nights now," said Margaret Newland, a local resident and mother of three. "But you have to wonder why he was allowed out on bail if he was already facing sex charges. The courts are supposed to protect people. Maybe if he had been kept locked up instead of being let out then that wee boy might still be alive."
Harris was supposed to attend a pre-trial hearing at Linlithgow Sheriff Court on offences relating to three girls aged between two and 11 years old, alleged to have been committed between 1993 and 2000. He had been charged with assault and lewd and libidinous behaviour, but released on bail at his first court appearance in February this year on condition he did not contact any of the girls.
On Sunday, officers went to Harris's house in Camps Rigg, Livingston, less than two miles from the woods where Rory's body was found a week earlier. Harris's body is thought to have been found in a garden shed. Lothian and Borders Police declined to discuss details of how Harris died, but said that they were not looking for anyone else in connection with his death.
Harris is not thought to have been convicted of sex offences, and there is no evidence that he posed a substantial risk.
Rory vanished 300 yards from Meldrum Primary School. He was last seen walking through an underpass to the school after his mother dropped him off in a layby.
In the biggest operation of its kind carried out by the Lothian and Borders force, a team of more than 70 officers has been trying to trace Rory's last movements.
Harris was not on the list of paedophiles interviewed by police immediately after Rory's disappearance. Officers were alerted by callers after appealing for help tracing a man wearing a black bomber jacket and waterproof trapper-style hat seen in the woods where Rory's body was found.
Forensic science experts have been searching the untidy gable-end house in which Harris had lived alone since his mother, Betty, went into a nursing home and his stepfather, Walter Inglis, died three years ago.
Forensic teams continued to search the two-storey property yesterday and a blue and white tent was erected in the overgrown front garden. A police spokesman said investigations were still "very much ongoing", but would not confirm reports that Rory's missing school bag had been found in the house.
Neighbours described Harris as a gaunt and scruffy loner who acted in a "threatening" manner. Although he had lived in the area for many years, residents said they had not known him well and described him as unfriendly.
They said few visitors were seen at the house and those who did call " appeared to be drunks or down-and-outs".
Such was the state of Harris's home that several neighbours were surprised to hear that somebody lived there. "I thought it was derelict because there were never any lights on," one said. "You never saw anyone coming or going and the garden was an absolute mess."
Another neighbour, Wera Ely, said the events of the past few days had been "a terrible shock for everyone because it's usually so quiet here".
Brian Presswell, 45, a cousin of Harris, admitted that he didn't have a lot of contact with his relative, but said he believed that he was involved in drugs, both using and dealing, and "was always in some sort of bother or other". Mr Presswell, who lives in Glasgow, said: "Simon was a loner even when he was younger and he drifted away from the family when they all moved to Livingston more than 20 years ago.
"He was a bad lot who, as far as I'm aware, never had a job of any kind and who only mixed with his own sort.
"Simon, his sisters Janet and Helen and his brother Robert were brought up in Prestwick and moved to Livingston in the 1980s. His sister Janet has been married several times and has lost contact with the rest of the family as well. His sister Helen went to live in New Zealand.
"I knew Simon would end up in big trouble one day and though I'm shocked that this has happened, in a way I'm not surprised."Reuse content