BlueCrab, you are right that Burke was the other person in the house that night. I tend to leave him out of my calculations for two reasons: one, that LE pretty much cleared him as far as they were concerned, and two, that even if he had been abusing JBR, and had killed her, how would he have known to inflict the sexual wound to confuse the evidence of past molestation? I know nine-year-olds can be pretty savvy, but I think it takes an adult mind to think of such a thing.
And let's remember, the evidence shows that the killer DID inflict that wound, either before the murder, or during it (i.e., after the head blow, perhaps, but before death by strangulation had occurred).
That's why I think the molester HAS to be the killer. If someone else was molesting JBR, why would the killer want to hide evidence of that fact? Even if the killer KNEW FOR A FACT that JBR was being abused, it makes no sense that he/she would inflict that wound--it's his/her best 'reasonable doubt' playing card!