Theory based on opinion of detectives and statments given by numerous people:
I think both kids had a degree of attachment disorder
I think there may have been alcohol abuse in the home
i think there was verbal and some physical abuse over bedwetting and over dress up and pageant times
The pineapple was Burke's snack and Jonbenet grabbed a bite, causing a fight soon after arriving home
I don't know enough to have an opinion on who molested or fanatically cleaned her previously, but Patsy must have known enough to know something caused damage
I don't know if Jonbenet got the head injury for eating the snack or for causing noise and arguing with another kid or even for resisting being cleaned
I think she may have gotten a few marks on her neck during an attempt to get away or from an attempt to drag her unconscious from kitchen to butler kitchen
I think the cord was to get it over with and the stick used to jab because it was the same size as what caused previous damage
The wiping was fanatical wiping of released urine and maybe to clean the body and to have on new underwear
The blanket and gown may have had blood from a previous assault and would have been disposed of
The killer wore brown gloves and may have handled John's shirt while grabbing a brand new washcloth
I believe the note was an attempt to fool John and get him out of the house. I don't believe he ever handled the note but demanded that police be called while he got Burke and checked the room
He later caught on and knew where to look and decided to get attorneys
If he had left to go get money from his account he may have then been sent on a wild goose chase and Jonbenet would have went missing and he still would have had to get attorneys
There are many facts we don't know and only think we do plus dozens of secrets.
Yes i do think it is possible that an element of the ransom note was designed to remove the Ramsey's from the house maybe so the body could be removed - maybe in the suitcase, but then Burke also would need to have been removed before the parents set off to get the money - if it is possible to get money at that time of the morning - perhaps from friends who might keep such amounts in safes and the like - which would also explain the low amount. The perp may have expected the Ramseys to have called friends before calling police due to the nature of the threats in the letter.
John may have realised the ransom note was a time-buying ploy but not got the reasoning correct as to why and this is why he said call the police - thinking they were buying time to escape because it is too hard to get that money at that time of the morning - do US banks open at 8? because he would have been needed to be back by 8 to be there for a call potentially coming between 8 and 10. This is why John said he called the police because he did not have the capacity to block roads or airports.