Laini, you ask some very good questions, IMO.
Rather than answer them specifically, I'd like to give you my theory of what happened. I think my theory may fit some of your questions.
IMO, this crime was committed by someone abusing JBR, who did not want that abuse to be discovered. And in the days leading up to the crime, this someone had reasons to be worried.
JBR acting up. JBR refusing to do what she was told, maybe even moreso than normal. A mysterious 911 call placed on the day when JBR sits on the stairs (the spiral ones, maybe?) crying and saying she doesn't feel pretty.
Now, was this 'someone' the same 'someone' who was taking JBR to the doctor so regularly? I don't tend to think so, though others do. But though the doctor hadn't done a vaginal exam on JBR in quite some time (if at all--though I thought the list of her dr. visits showed one) PR was obviously concerned enough about JBR's vaginitis to seek medical care. It doesn't completely exclude her as the killer, but I think it makes JR more likely, since he wasn't the one taking JBR to the doctor.
So let's pretend that JR is the killer. On Christmas night, something happens that makes the problem of JBR something he has to take care of right away. (There are several possibilities, but this is already going to be too long.)
I do think there was a rage element--that blow to the head required powerful force and an intent to kill, in my opinion. But behind the rage of the moment was fear--and it's interesting to me that JR's sudden shift from 'nice' to 'angry' has been as easy to see as PR's was, in interviews etc.
Once the blow to the head was struck (along with some other 'manhandling' incidental to that, imo) JR realized that he was going to have to finish the job.
I think he took her to the basement at this point, no matter where upstairs the initial blow took place. I think he inflicted the sexual wound, which does appear to have been inflicted while JBR was still alive, in order to compromise the evidence of earlier abuse (and it worked, btw.) I then think death by strangulation took place--just a simple rope, no garrotte, 'elaborate' or otherwise.
Then the first staging took place. It involved a few things: BR's knife left by the rope's edges; a golf club beside the body; and the replacement of JBR's underwear with the size 12's, to hide the sexual wound which had begun to bleed and had possibly stained the other underwear.
JR then wakes PR, tells her to dress. She throws on her clothes from the night before and follows him. It is her scream the neighbor hears.
JR tells PR that BR is responsible for the crime. He struck her once before with a golf club, the two of them fight like normal kids, and the scenario he has set up is very plausible. Later, he will tell her that BR has no memory of what he's done, something PR will believe because she wants to believe it. Maybe JR even says that they have a responsibility never to tell him what they 'know' in order to help him 'heal'. But at the moment, their concern must be for him, to protect him.
Now, whether or not PR knows CO law won't let BR be charged in the crime doesn't really matter. Maybe she does, and her motive in helping with the cover-up is just to keep BR from being taken away from them, as he most likely will be. (JR has a powerful weapon here: he just has to hint that social services will get involved and take him, and that PR's cancer could return and she could die without ever being allowed to see him again.) But she does agree to help.
JR sets her to the task of writing the ransom note, probably telling her certain things he wants her to put in, but leaving the rest to her. He then goes down to prepare JBR for what he intends to do: he intends to dump her body somewhere. (Indirectly corroborated by the RN writer's possible subconscious concern about a 'proper burial'). He definitely wants to dump JBR's body; the best scenario for him at this point is that her body decay to the point that the sexual abuse isn't noticeable at all. Unfortunately, things have taken too long. If PR saw the body around 2am (scream) and it took an hour or so to get her composed and get her started on the note, then it's around or after 3 by the time JR gets back to work.
He's supposed to re-dress her in the Barbie gown and wrap her in the blanket. Unfortunately, if the crime occurred sometime between 11pm and midnight, as I think it must have, it's now been three to four hours since she was killed, and rigor mortis has started to set in, enough to make it difficult to replace her clothing. Not only that, but JR has had time to think about the 'dumping the body' scenario and has realized that there's no way to do this undetected. It's just too risky, esp. with that 7am flight scheduled, the cancelling of which will definitely raise questions.
He re-stages JBR's body to look like the work of a sexual pervert instead, hoping that this will erase any questions about sexual abuse. When he fashions the garrotte, the fibers from PR's sweater, which are all over the rope due to the time PR spent holding and sobbing over JBR's body, are twisted into the knot.
He goes up to PR and tells her what he's done, telling her, too, that it will be better for him not to give her details which will only be upsetting. She has finished the note; he decides they must use it anyway, since he has to have a legitimate reason for calling the airport and cancelling his flight, and he's smart enough to know that just not being able to locate JBR in that huge pile of a house isn't a good enough reason, since if she's just missing, they'd obviously have to pretend to search every room for her, and would then 'discover' the body too soon as well.
By this time, I think it's at least four a.m., possibly closer to five. They spend a little more time getting things 'ready' and if my experience of women like PR is any guide, it takes her almost half an hour to put her makeup on anyway. They also rehearse for as long as they dare to: the call, their story, as many things as they can think of. They didn't do a very good job of this that first day, though, did they?
Finally it's time for the 911 call, about the missing daughter who isn't missing at all.
Things will happen later that make sense by this theory: JR's 'walk' alone the night of Dec. 26 (to dispose of the underwear, maybe?); JR's concern about the golf clubs, which don't appear to have any real connection to the crime; the fact that BR's knife was found near the crime scene, and some other oddities that crop up.
I think this explains the odd discord between the RN and the crime scene, but obviously there are many other possibilities.