In my tinfoil-hat-opinion, the ransom note was Patsy's doing, and not part of John's covering up of the crime. Naming his bonus amount was a way of throwing a monkey wrench into the "official" Ramsey alibi. The amount would redirect police attention back onto John Ramsey, hopefully uncovering his late-night parties. It was her revenge on him for (indirectly) killing her baby girl.
Yes, that's certainly a very tin-foil-hatty opinion. But in your defense, this whole story is so bizarre that whatever the truth is, it will sound like a total tin-foil-hat hallucination (if we ever get it).
I see no reason to believe the parents had anything to do with this. We have seen this over and over again since this case. Some pervert takes the child out of the house-or kills the parents and takes the child.
Which one of them, John or Patsy, raped her with the blunt end of a paint brush and why do you think they felt this was necessary?