I agree with you, UK, that the head bash and sexual assault likely occured simultaneously, with the assault causing JBR to scream, and she was then bashed on the head to silence her quickly. I do not think she was bashed to kill her intentionally. But that fatal act having taken place, there was no turning back for the Rs. We may never know if both parents were there at that moment. Remember it has been noted that although the head bash would have knocked her out instantly, death could have taken at least an hour after that. Faced with a dead child on their hands, AND a dead child that at least one parent knew had been sexually assaulted, I believe the strangulation was done to provide a VISIBLE means of death. I think the Rs may not have realized that an autopsy would be still be done if the garrotte was there and she LOOKED like she had been strangled to death. I have read that this was a "gentle" strangulation, with no breakage of the hyoid bone and no damage to the internal structure of the neck. There was only the ligature furrow and petachiae, and though the pressure of the garrotte on the vagus nerve could have caused her to lose consciousness or stopped her heart, I do think this was staging.
As far as the time of death, that was a very useful link. TOD is always relative and dependent on many factors, BUT if the coroner or his team had done the simplest tests mentioned, the liver stab and eye fluid test, they would have had a closer estimate. It looks like all this guy did in his 10 MINUTES with JBR was pronounce her dead. One wonders if he held a mirror to her nose, as they did centuries ago, and that was it.
As far as the position of her arms being changed AFTER rigor, this did not happen for this reason- rigor can be "broken" but it is difficult, and will not re-form after that. The coroner did note rigor in her ams and legs on the autopsy.
I think even with the lax testing of the body, we still have a good idea of when she died. Rigor suggests midnight to 2am as the TOD, so do the stomach contents. When she was "found" at 1pm, in full rigor, that would be about 12 hours after death, exacly in that window of time needed for rigor to form. All digestion stops at the moment of death- nothing moves along in the digestive tract OR is broken down by stomach acids or enzymes after that. So where the pineapple was found (in her small intestine) and where the soft green fecal material was found (the Christmas meal) would also coinside with the TOD suggested.
Now, if full decomposition takes place, that is another matter. Then the contents of the digestive tract will decompose along with the rest of the organs and soft tissues of the body.
The livor mortis also suggests she was not moved shortly after death, as it was fixed (non-blanching) and if she had been moved, there would have been a secondary livor pattern noted. You can clearly see on the autopsy photos the white "striping" effect on her back where the elastic of the underwear and long johns touched her skin, and where the wrinkles and folds of her shirt pressed against her back. She was redressed right after death, and the shirt may have not been removed in the first place. Livor begins forming very soon. If she had been redressed after that, there would be no white marks on her back. It is possible for the body to have been moved after livor was fixed, and if it was long enough after (like 10-11am the next morning when JR "went to get his mail and ADMITTED to being in the basement at that time) he could have moved her then without a new livor pattern forming and without breaking rigor.