I agree the ransom note was written to draw attention away from the house, with the purpose of giving the perp an opportunity to remove JB's body away from the house, as well as provide for a reason to find her dead. The note is constructed to provide an opportunity to take her body out while JR goes for the ransom money, IMO. I believe the note writer acted alone, and the intent was to fool and scare the other parent into co-operation with what appeared to be a kidnapping. I also believe JB was simply going to be taken out of the house in a car and a call to police when she was "picked up" would be to summon them to the pickup point, where she would still be in the car (along with some local debris). Because it would seem likely the finder would lift her up thinking she was alive, then could lay her in the car while making the call to police. That would account for any forensic evidence found in the car, and allow for her to have a proper burial. The problem was the phone call made to police at 5:52 a.m.
If it was Patsy acting alone, and JR told her to make the call, she would have had to go ahead with it, or else JR would have done it. Better she do it, and get the theatrics involved. If it was JR acting alone, PR made the call before he could get her stopped. Either one of those scenarios work. And there were accounts from them of it being JR's idea, and also of it being PR's idea.
Now, please bear with me as I think through some theoretical processes of how either of the two R's might have pulled it off.
If it was JR acting alone, and PR would not have made the call, he could have sequestered PR and Burke off somewhere safe, providing him complete opportunity to get JB's body out of the house and proceed with the ransom demands, even to the point of "talking" to someone while being monitored, which would have secured JB's death by the Faction. Of course, they would have collected the money before advising him of where he would go to "find" his daughter, thinking she was still alive. Which means he would only have to place the brown bag somewhere to leave forensic evidence, then could have just simply kept the money hidden away elsewhere to be used later. A multi-millionaire has no problem wielding hundreds and twenties as spending cash. He would later tell police he drove to the pickup place immediately, thinking JB to be alive and would not want to jeopardize that. But upon arriving and lifting her up to find her dead he would say he laid her into the car, so he could then make a call to police which would then set up the intruder kidnapping/murder. And, oh, he might have even produced another note from the kidnappers which he would have found at the money drop spot, with directions on where to find JB. Maybe some of those missing pages from the note pad?
If it was PR alone, she could have taken JB's body out of the house as soon as JR left to collect the ransom money, simply putting her in her car, waiting until JR had gotten home. Burke would have been told to stay in his room, where he would be safe, until JR returned. PR would say she received the call (at the house) from the kidnappers saying they saw him get the money, and JR would transfer the money into the brown paper bag. The "kidnappers" would have given instructions to Patsy for John alone to make the money drop and would be "exhausting". This would leave PR the opportunity to get another call from the "kidnappers" once they had picked up the money, with instructions where JB could be found. Instead, PR would be right behind JR, and she would abscond with the dropped money. JR would head home to await further instructions but come to learn PR was already involved. She would have driven to the "pick up" location, under the ruse of having gotten another call from the kidnappers once the money was delivered as to where she could find JB. Once there she would phone the police (and JR) to complete the picture. The only problem I have in this scenario, is what does she do with Burke when she would have to drive away to supposedly "pick up" JB? Of course, at this time, it should have been safe for her to call one of her good friends to come and stay with Burke, since the drop would have been made and JB should have been found safe.
All too far-fetched? Did I miss any major points? Of course, I don't think either of the R's would have thought far enough ahead to realize phone records might be checked and they did not think there would be a requirement from LE for an autopsy on a child who obviously was horribly strangled by someone from a kidnapping Foreign Faction. I believe the perp intended to set JB's death as an obvious strangling, with the clean up of the sexual assault and the head wound to not be discovered, in order to dismiss any thought of requiring an autopsy. And I believe that either of JB's parents would have assumed they had any connections they would have needed in place to make their plan work out the way they had intended....except for that call ending up being made when it was.
My bet would still be on JR, but then, there is the convincing work done on the ransom note by Cherokee on FFJ and supported by several top handwriting specialists. The one problem I have, though, is there was so little handwriting comparison made available to the public from JR. We should have been able to see as much from him as we saw from Patsy in order to make more assessments of our own. I would want to see more of JR's to see if at other times he was confused as to whether or not to use a single or double "s" in certain words, like his exemplar showed in his spelling of the word "occasions". Especially since the ransom note had 2 words with double "s" misused. And for anyone else who might wonder if JR actually could have written the note and has not seen it, you might find this interesting:
http://solvingjonbenet.blogspot.com/2012/07/some-handwriting-evidence.html