as for your questions, I can tell you the answers from what I know to be fact and from my perception of the case.
For the defense, the points I am uncertain still on, is 1) was meredith moved later, and if so, how much later, or if that is unknown. 2) Were Rudy's footprints laid out in a pattern of running or walking out the door. 3) Was there any indication of wiping away blood in the bathroom or the hallway. 4) The exact scientific data on luminol enhanced footprints, why no one elses footprints luminsced, and when exactly was that luminol testing done. 5) Whether or not the knife originated from the girls apartment or not definitively. (I know they found it at Raf's apartment).
1. I think she was moved, but not much later than the fight. I believe she got stabbed by the waredrobe, a stab that brought her down to the floor, and as she laid there bleeding, RG got the sheets and pillows off the bed and dragged her into the final position they found her in. At that point, he could have also went to get the towels from the bathroom or something. the blood drops on her breasts are supposed to indicate that while on her back in her final resting place, she was still breathing. I believe this is when he took off her pants and panties, which you see right by her feet in the murder room, and he attempted to rape her. maybe it was even at that point when he realized what he'd done to her and he couldn't stay erect anymore, and maybe went to get the towels to help her at that point. I don't know.
He could have even had the thought that he'd call the ambulance after he got far enough away but then just got scared and chucked the phones. He could have tried to call the ambulance right there in the house with her phones and that's what the "playing with the phone" was all about. When he couldn't get them to work, he just left with them and chucked them. I don't know. He could have stolen them because he stole phones before. He had a backpack with some in there when he was caugh at the nursery--people's keys, too.
2. RG's left shoe print made a circular pattern on the pillowcase as if he was struggling with her or perhaps struggling to move her over into the final position. then there were 3 prints that I interpret as him going over to the bed, where he could have taken the time to go through her purse, which was on top of the bed that now has no bedsheet on it. Next, his left foot print fades as he goes out the front door. There is NO right footprint accept the barefooted one on the bathmat, which is a strong indication to me that RG somehow lost a shoe in the struggle. I think he then removed both shoes and walked to the bathroom. While rinsing his jeans or bloody right foot, or hands, whatever in the shower or the bidet, he put his foot on that bathmat, making the watery blood prints. To me, that toe looks obvious dissimiliar to RS's distinct hammer toe, but you have to look at it through your own perception. The Defense makes a good case for botched measurements etc of the print.
3. I do not believe any blood was wiped up because, as you already said, we'd see those wipe marks and not clear prints if someone had wiped something off the floor or another surface.
4. I don't know what date the lum. testing was done, but there has to be something either on the floor or on the foot or shoe to make it show up. I don't know if they did the floor of the entire cottage, either. You can see spect like substances on the floor tested, which they think is the detergent from prior cleaning. I think the prints in the hallway could be AK's from showering in the murder bathroom and stepping on RG's footprints, but the test for blood in those prints came out negative. Additionally, the investigator who did that test tried to hide that information from the court until she was forced to hand it over half way through the trial.
5. The kitchen knife came from RS's kitchen. So the prosecution had to figure out why or how the knife got to the cottage to be involved in a crime of passion murder. They came up with a very stupid reason, if you ask me.