Handwriting evidence is weak even when they say they've got a match, "can't be excluded" means very little to me.
I think he was a pedophile who followed the child pagents, as part of his fantasy life. I think he may have to some degree known of the family. I think he planned to kidnap her, get some nice ransom money, and have a child to rape for a few days. I think he thought he knew her, just like a deranged stalker of a movie star thinks they know the movie star - not that he did know her. You know the type of thing - "The way she posed at the end of the runway, that was just for me!". I think he wrote the note, went up and got JBR, saw the tools of his trade - or at least something he could easily adapt into them, decided to go for it, and bashed her head when she wasn't responding as in his fantasies, dressed her as his little doll, or maybe not realizing she was all the way dead, not just unconscious at first, and left.
DNA in a dead girl's panties, liquid, in blood - that's insanely strong evidence to me. Only the fairly unlikely possibility that it was from manufacturing made it possible to ignore. But when you add in that exact same DNA being elsewhere on her clothes - that possibility vanishes, and to me, you are left with the clear and unconditional fact that this is the killer.
There are a few options there that include the parents - but that is one of the killers at the very least. Someone could say they knew and allowed it, and wrote the note to cover - but that sounds too improbable to me, without any evidence of it.
Not so long ago, many believed poor Jessica's father or grandfather killed her - it was too improbable that someone snuck into the house, and the grandfather just so happens to have had related problems in the past. If Couey had never been found, they'd still be considered no doubt guilty by some - the coincidence of a dead girl with a questionable family would be too much.