I don't see any glaring errors here, but there are others who know the case better than I.
Ron Hendry (you can google him) makes a good case for both the break-in and RG as a lone assailant.
Most of your questions are answered if RG is on the toilet and surprised by MK returning home.
I think I pretty much understand where the facts lie now. I'm kind of playing devil's advocate on both sides, but if I'm honest, the things that actual trouble my peculair way of thinking are these, in order of concern. :
Againt the Defense:
Why no one showed you could climb THROUGH the window. (did a full physical recreation). Why only her bare left foot flouresced in the absence of other people's feet. Why is there no DNA of Rudy in the bathroom. Why would Rudy lock Meredith's door. Why would Rudy steal the phones and then throw them away. And I do find it a bit suspicious that Raffaelle was a knife aficionado. AND, even with the new report, how did Raffaelle get unlucky enough to have his DNA migrate and not someone elses. (Though it appears the report may be saying that the DNA is not provable as his, I'll reserve this point until after I read it.)
I am not really concerned at all about anything else. But I would imagine most people would find her testimony troubling. I just don't.
For the prosecution, my concerns are:
The evidence of bias by the DNA team (using methods they shouldn't have, using suspect-oriented thinking which I think is clear.) The evidence of bias by the police (which always happens, but generally causes errors), the lack of bloody clothes associated with the defendant, the fact that the knife wounds match a knife Rudy owned, the tight room space that the murder would have to be committed in, the lack of pre-meditation by the defendants, the lack of ability to collude prior to the murder for the defendants, the lack of motivation for a murder. Why, if Amanda was told Raffaelle was selling her out, would she point the finger at Lumamba instead of Raffaelle? The assumption that there was a thorough clean-up yet they missed the bloody footprint. Why, if they were staging the scene, wouldn't they both have "discovered" the body and called the police, so as to explain why their DNA might be in the room?
Edited to add: And the fact that they had only been dating for a week, and everyone agrees they barely knew Rudy.