You know when kids break things and commonly they try to hide what they broke to try and hide what they had done? My theory:
Burke hits JB over the head in a rage over something, perhaps the theory that she stole some of his pineapple snack. Fractured skull, brain bleed... she's not waking up. So he freaks out. Makes himself a toggle rope using his boy scout knowledge and attempts to 'hide' JB in the basement. This process inadvertently kills her by preventing blood flow to her head as he's dragging her down there. Parents wake up, eventually find out what happened. Oh ****, our ****** up son just killed our daughter. Patsy is freaking out, she's just found out her cancer has returned and has made the realization that Burke will be institutionalized for longer than the period she potentially has to live. She just lost one child, she may lose another. The father on the other hand knows the news of this will probably put him out of commission. So they (poorly) fabricate a kidnapping tale and the rest is history.
Things of note:
1. Burke had a history of acting out in a rage. He had hit JB over the head with a golf club previously, leaving a scar.
2. Several 'my son needs help' type books were found in the house. I think the family knew Burke was a lose screw.
3. The 'taser marks' were likely made by a piece of his train set whilst poking her in a childish attempt by Burke to wake her up.
4. The unknown DNA profile found on the underwear, two theories: either DNA picked up from the carpet whilst Burke was dragging her, or someone left it accidentally during production.
5. Not sure what to make of the vaginal scarring, I'm not going to get into potential sexual abuse however predators have been known to be involved in the child pageant industry in which she was apart of.
6. The empty suitcase found near her body, perhaps was to be used to move her outside the house to be hidden elsewhere. The parents probably didnt have the heart to treat their child like that and left her where she was instead.
7. Speaking of suitcases, what to make of the other suitcase found in the basement that had two items: a semen stained childs blanket, and a bunch of childrens books? The semen DNA matched John Ramsey's son from a previous marriage.