In a nutshell without getting lost in the details, BR manually strangled JonBenet and sexually assaulted her, he may have whacked her on the head to silence her? Consider Coroner Meyer's remarks about
Sexual Contact and
Digital Penetration.
The parents then attempt to hide this by staging their own version, applying the ligature/paintbrush, and using the paintbrush to assault JonBenet internally?
It might have been one of the parents that whacked JonBenet on the head and as JR suggests this failed so she was asphyxiated?
If you think the train tracks were used then these and the paintbrush should help you to partition the house into a Primary Crime-Scene, i.e. BR's locus, and a Secondary Crime-Scene, i.e. that of the parents: basement.
So you have the train tracks upstairs and the paintbrush downstairs:
Linda Hoffman-Pugh said she had left the paint tote at the foot of stairs on December 23, and didn't know who had moved it?
So although there might have been some intermediate staging or events we know nothing about.
An occam or kiss version of events, has JonBenet being assaulted upstairs and the parents staging it away downstairs.
I do not think BR was involved downstairs, there is
no forensic evidence linking him to JonBenet in the wine-cellar whereas there is for both parents, but BR is linked by all the circumstantial evidence to events that night, pineapple snack, those pants in JonBenet's bedroom, etc.
To speculate further in an attempt to highlight that JonBenet and BR were likely meeting regularly at night.
Those pictures that were dumped into the basement might have actually belonged to BR and not JAR as previously suggested, i.e. it may have been BR who was obsessed with JonBenet, and for all the wrong reasons?
.