I too don't think John was clueless. For the fibers from his shirt found in the crotch area of JonBenet's size 12 undewear implicate him in the staging of the scene.The problem with the clueless John theory is that he colluded with Patsy as early as the 911 call, by claiming Burke was asleep, when actually, Burke was out of bed and in distance of the phone. IMO he would have to know WHY he was giving a false version of events to police.
Also, I don't think Patsy would have been able to carry out all the staging alone. I believe the psychological strain would have been too much for her. Aside from that, in order to do all this, Patsy would have to be gone from the common bedroom for hours. Suppose John woke up, saw that Patsy was not in her bed and she did not return, wouldn't he have gotten up to look for her?
I believe John covered up for Patsy way before 10 am the next morning.