Logically, I think guilt stands or falls with the fact of staging/simulation, even making consideration of dna/blood/luminol/knife evidence - and even the clean up - less relevant.
For if the burglary and sexual assault were simulated (as has been set forth by the prosecution and ruled by Massei), then it can be inferred backwards that someone had an interest in doing this, and it was not likely to be Guede.
If AK and RS were present when MK was sexually assaulted (the evidence suggesting this, and only this, for no evidence suggests that either of them sexually assaulted the victim) then it can be deduced that it was the consciousness of this assault (having been present when it transpired) which would give them the idea to stage a sexual assault once the victim was deceased, (removing the bra with a knife, and pushing the shirt up) to mislead investigators about their presence, and to lead them to believe that a lone wolf and not a threesome were the perpetrators of ANY violence.
Furthermore, the staging of a breakin and burglary would again seem to lead away from Guede-as-lone-wolf and toward Knox and Sollecito.
If there was no staging/simulation, the rest goes falling down into nothing. And this must be concluded from determining facts such as if the bra was removed after or prior to death and if the rock was thrown from inside or outside the window. If I were on the jury, this would be my obsession right now, to rule out reasonable doubt.