I have a few thoughts from the clues Kolar gave.

I am leaning toward John maybe not being aware of murder until he found her body at 11:00. From there, he somehow put the pieces together rather quickly that Patsy was responsible, remembering that her handwriting looked familar along with the phraseology. This might explain why he was so distant from Patsy that morning and told Arndt it was an inside job. Once he and Patsy were alone, she confided in him and that is when the real cover up began.

The only other thought I have right now is about the pineapple. As far as we know, JonBenet's fingerprints were not on the spoon or the bowl. She might have grabbed the pineapple out of the bowl with her fingers while Burke was eating it with the spoon. This might account for why animal hair was found on her hands; they were sticky. Maybe it was at this point that Patsy grabbed her by her shirt collar and told her to behave, leaving the red mark on her neck. Maybes Burke tried to strangle her with his hands.

Maybe the kids were alone in the kitchen alone and that is why the grand jury said the Ramseys had put her in a position of endangerment in that a six year old and a nine year old were a volatile mix.

I think the torn wrapping paper held the large panties that Patsy intended on giving to her niece. When the cops took items in the warrant, that pack of panties was not in the drawer with the rest of her regular sized underwear. I do not think the cops would have missed them.

I don't understand Kolar's comment that the strangling and garroting were not staging but part of the motivation for her murder. His use of the word motivation is very interesting. I don't have any ideas about the role the train tracks played, although the points do line up exactly with the marks on her back as opposed to stun gun marks that do not line up. I suppose the marks could have come from her body laying on that portion of the track at some point in time but the piece of track would have to had been laying in the vertical position.