#1 and #2 were definitely thrown out in the appeal because of the C&V report and testimony.
There was little to no dna or more importantly blood found on the knife. The crime scene investigator Stefanoni broke protocol and magnified the machine way past what it is intended to come up with something linking Amanda to Meredith's death.
(When this is done the machine picks up any and all dna that's been in the machine, which included Meredith's blood from the crime scene and explains the result.) This is not accepted by anyone that does dna and would have never been allowed in a us court. It was just too small a sample or didn't exist at all, the latter being likely. Not to mention that the knife didn't match the blood outline of the murder weapon at the crime scene and it wouldn't have made all the wounds. Which is why the prosecution had to make up the second knife scenario. It also didn't test positive for blood, kind of a must if you need it to be the murder weapon. It was also randomly picked by the police and was the only knife tested out of all those in the girl's apartment and Rafael's apartment. Kind of suspicious don't you think?
Bra clasp wasn't found until they went back in months later. Coincidentally the day after Rafael's father went on tv and shot down the previous evidence that supposedly linked Rafael to the crime. Two of several bloody footprints found in the murder room were originally linked to Amanda and Rafael by the prosecution. But those prints ended up being partials that were from the same shoe that left the others. A nike pair that Rudy Guede still had the box for in his apartment. The shoes though were never found, most likely dumped in Germany.
Back to the bra clasp, the police's own video showed where the clasp had been touched and passed around with dirty gloves and then put back on the floor which is a contamination no no. They ended up having several dna profiles mixed together according to C & V and Stafanoni cherry picked the ones she needed to link Rafael to the crime. C & V said that she could have found her own dna or even the judges dna in the sample by cherry picking also.
On the bloody footprint on the bathmat. I can tell you that the prosecution says it's Rafael's footprint. Footprints aren't like fingerprints, so there is no concrete science to prove one way or the other. But just looking at it, it appears to match Rudy moreso than Rafael who has the hammer toe. I know that the prosecution tries to say that it measures to be like Rafael's but I don't think there is anyone that can identify by size its very easy for a print to be just a partial which is going to make the size smaller. Also how could it have gotten there if its Rafael's? There is no evidence he was even in the room so how did he get in the bathroom and then all of a sudden leave a bloody print? Makes more sense that the guy that was bloody was Rudy and it's his print.
The bathroom sink is the only place where Meredith's blood and Amanda's dna is found together. It's perfectly normal for Amanda's dna to be in her own sink where she brushes her teeth etc. Rudy washed Meredith's blood in that sink and that's how you get mixed dna samples. There is even police video tape where the crime scene investigator makes large sweeps for their samples in that sink which increased the chances of mixed dna. There was also some dried blood drops of Amanda's found on the faucet which were likely from her pierced ear prior to the murder. There were never any signs of cuts on Amanda or Rafael. There were no signs of a clean up. If bleach is used in a clean up it still lights up with luminol in the wipe spot. Rafael's housekeeper said that the bleach in his home was still the same from when she last used it also.
There was a dna blob found in Filomena's room or outside it. This contained dna not blood of Meredith, Amanda, and others not tested. Most likely the other roomates. It's totally normal they live there and shed skin cells and have saliva and hairs etc.
The luminol prints were in the hallway, they were not leading from the body or Meredith's room. Luminol lights up to many things including bleach but also cleaners that contain bleach or other chemicals. Those prints weren't necessarily Amanda's, they could have been any of the girls and could have been from someone walking out of the shower that had been cleaned recently. There is nothing to show that they were even connected to the murder. They were tested and were either negative for blood or didn't contain dna.
I already covered it but the print was another partial of Rudy Guede's nike shoes that had a circular pattern. Since a partial is smaller the prosecution tried to link them to Amanda and Rafael.
There were no signs of clean up. To clean up blood you need bleach, bleach lights up luminol. It's also impossible for two people to be involved in what was a very bloody crime to clean up every bit of blood and leave none of their dna, fingerprints, or hair and not injured themselves and yet leave plenty of everything of Rudy Guede, who did leave plenty of dna, hair, fingerprints at the scene. This why the defense attorney even mentioned that they had magic soap. I guess it was a good thing that Amanda was a witch.
If you don't know already. Injustice in perugia has all the information and pictures that explain things. Included is a former FBI agent Steve Moore who also has a blog. Moore isn't the only expert from the US convinced that they are innocent.
http://www.injusticeinperugia.org/
http://gmancasefile.blogspot.com/2011/10/amanda-knox-innocent-girl-finally-goes.html