best scenario defense:
for break in: Rudy opens shutter, or shutter slightly ajar so he can throw a rock through to see if anyone is there. He breaks into house through front door, then goes to the room to close the shutters so you wont' see the broken window. In the dark, he bumps and stumbles, scattering clothes on the ground. When he reaches the window and opens it to close the outdoor shutters, glass falls on top of the clothes. Alternatively, he spiderman scales the walls, comes in through the window, stumbling in the dark and scattering the clothes, and as he shuts the window/stumbles against it, glass falls on top of them. Alternatively, in the chaos of the moment of discovery, glass gets shuffled on top of things. Alternatively, Filomena is under stress and later suspicious of Amanda and so her memory is tainted (unintentionally) of the condition of the scene.
He drinks orange juice, takes a dump. Meredith arrives. He either pretends someone invited hi there and he is with them or he remains hidden in the bathroom. He sees that it is Meredith, alone and becomes sexually excited about the situation. Or perhaps he came here looking for the girls in the first place. Meredith, feeling suspicious, discovers the broken window in the room. She runs to her bedroom to call the police using her cell phones. Rudy emerges, giving chase with his knife. He attacks her from behind and there is a struggle over phones. He attacks her from the left and the right, alternating blows (because he is trying to get the phones?) As she collapses to the ground, he attempts to sexually assault her. She manages to get to her phone and he hears it make a connection which panics him. He grabs the phones from her and flees, and tries to see if she called the police with them. Fearing he can be tracked using the phones he throws them in the garden. He waits to see if he's in trouble, having left his stuff behind. (In Filomena's bedroom?)
He returns to get his things. First he goes into Meredith's bedroom and quickly grabs what looks valuable from Merediths purse, but does not rob anything else because he is worried that someone could come in at any moment. He finds her keys in her purse, and locks her door before he leaves. (Unless the door can be auto-locked without the keys). He throws the duvet over her. He locks the room so that if someone comes in while he is cleaning up in the bathroom, they won't see murder.
He quickly cleans off the obvious blood so he can walk down the street without looking suspicious (He is not interested in cleaning up the scene). The bloody footprint in the room is his, masked by the soft pillow. The blood spatters in the bathroom are his, as is the bloody footprint, the toe of which, through bad luck, appears to look more like Raf's. He does not track bloody sneaker prints back in because the blood has completely dried on his sneakers at this point or because it is washed off from being outside.
Amanda arrives the next day to get ready to leave for a trip with Raffaelle. She is slightly concerned about the state she finds the house in, but takes a shower anyway. She steps in something that causes the front half of only her right foot to flouresce. She takes a mop to go back to her boyfriends to clean up a floor that was dirtied 14 hours beforehand. They then return and call her roommate to report a break-in. The CCTV footage incorrectly makes it look like they didn't call the police, but they did. Amanda fears that the burglar might still be in the house, and realizes she might have been murdered as well, so she takes comfort in the arms of her boyfriend. She can't understand the language and so hangs back and communicates to the officers in a mangled way that they find suspicious.
She is then taken into custody where, after lengthy questioning (and in response to police pointing out a text from Lumamba) that Lumamba is responsible. She then states shortly thereafter that this statement does not feel real to her.
Meredith's DNA on the top of the knife happened because Amanda brought it to the house for some reason, or because of contamination or because the police planted it.
Raf's DNA on the bra strap happened because of contamination, poor protocol, or because the police planted it.
To believe this scenario you have to believe:
1) Either a convoluted story of the break-in (see above) or that the break-in was real but left little evidence of disturbed ground, marks on the building, and happened in a less desireable break-in point. OR that Rudy would stage the break-in.
2) That Rudy would flee and return. OR after murdering meredith he went to the bathroom without leaving prints, washed off, returned to her room, got his stuff, and then abruptly fled without robbing any more (because he was worried she'd called for help on the phone?) Note: his shoe prints could have become bloody the second time he entered the room. i.e. he went to the bathroom, cleaned off, came in and tried to stop the bleeding... which is when his shoes became bloody.
3) That Rudy would have alternated knife strikes from one side to the other. And a scenario where he would also disrobe her. The Messai report does a good job of making this seem extremely difficult.
4) You must believe two piece of evidence were planted or tainted.
5) You must believe two pieces of evidence are incorrectly identified. (footprints)
6) You must discount several bizarre statements given by the defendants. (false accusation, a really weird story about a mop that however appears to not have been used at the murder scene, and a really weird shower story that involves hopping around and using a bathmat as a towel that appears customized to the exact evidence found... i.e. hopping and sliding on bathmats and explaining a drop of blood.)
Ironically, the part I find the weirdest is the earrings part since she had no cut on her body, so explaining why her blood is in there does not have anything to do with anything. Except perhaps helping the prosecution, because they can say all the evidence in there came from the 24 hours around the murder and not prior to that. Then again, she could be crafting her stories to match exactly everything she sees...
I will say, again, that in my own experience, I actually did create a story to match the evidence I saw, but attributed it to my own memory. When I was shown video, I realized I was wrong. That was in a car accident situation though.