MK's DNA was found on the knife in RS's flat
The test was invalid. Precautions against contamination were not taken. The laboratory was not certified for carrying out low copy number DNA testing. The correct procedures for carrying out the test were not followed. There is therefore no valid scientific evidence that MK's DNA was on the knife. Also if, as the police claim, this was the murder weapon it is too large to have caused the wound if thrust in up to the hilt. However, the entry wound is consistent with a knife being thrust in up to the hilt. The prosecution's explanation is that Knox was holding the knife by the blade rather than by the handle when inflicting the fatal blow but managed to do so without injuring herself.
DNA was found in Fillomena's room
They found Kercher's DNA with a very weak profile for Knox. They shared an apartment. What other explanation do you need?
MK had to have been held down
That is the prosecution case. Many experts have said that the injuries are consistent with Kercher being rapidly overwhelmed by a violent attack.
The fake burglary
If it was fake. The evidence for the burglary being fake is at best weak. Contrary to your statement it has NOT been accepted as false by all sides.
The confessions
A common feature of miscarriages of justice sadly. At no point did Knox confess to murder. She did implicate Lumumbu. Her statements were inadmissible as evidence due to the circumstances in which they were obtained. As is common in miscarriages of justice, the statements were consistent with the police's theory at the time they were made but did not match the facts of the case.
The call to the police not being made, but calls to Seattle and RS's sister were
If we accept their version of events neither Knox nor Sollecito knew that Kercher was dead at this stage. They had found the front door to the flat open, windows broken and blood in the bathroom. They had attempted to call Kercher and Filomena. After Knox's mother advised them to call the police they did so. Perhaps many people would have called the police first but I don't see anything particularly suspicious in this.
The mobile phones and the bomb threat
You are aware that the bomb threat was entirely unrelated? And that the mobile phones belonged to Kercher? Are you suggesting that Knox and Sollecito discarded Kercher's phones then rang one of them to alert people to its location?
RG's conviction is that he was not acting alone, can he appeal now
No. He was convicted of murder. That conviction stands. The forensic evidence clearly shows he was present whereas there is no forensic evidence placing Knox and Sollecito at the scene.
The prosecution theory is something like this:
Guede frequented the downstairs apartment and had a passing acquaintance with Kercher, Knox and Sollecito. Kercher invites Guede to the apartment. Guede defecates in the bathroom but does not flush the toilet. Knox and Sollecito return to the apartment. Knox discovers the unflushed toilet. Tensions between Knox and Kercher over cleaning the apartment come to a head. The row escalates into physical violence. Kercher is stripped. Guede restrains and sexually assaults Kercher while Knox and Sollecito attack her with two knives. One of the knives is Sollecito's penknife (as far as I am aware this was a new theory advanced at the latest hearing with no forensic evidence in support). The other is a kitchen knife from Sollecito's apartment (sometimes referred to as the double-DNA knife) which, it is alleged, Knox carried with her for protection. Note that there is no evidence for Knox carrying this knife. It is pure invention by the prosecution to explain how the knife got to the murder scene. The attack continues until Kercher is dead, the fatal blow being inflicted by Knox using the kitchen knife which she is holding by the blade. Some or all of the three then stage the scene to look like a break-in. Guede leaves. Knox and Sollecito clean the room, moving the body away from the wardrobe and removing all forensic evidence of their own involvement but leaving significant evidence of Guede's involvement. At some point Sollecito removes a shoe and sock, gets blood on his foot then hops to the bathroom where he leaves a bloody footprint on the bathmat. Knox and Sollecito then return to his apartment taking the knife with them. They clean his apartment with bleach. Presumably they dispose of the clothes they were wearing as well since no forensic evidence was found on any of their clothing to link them with the murder. However they do not dispose of the kitchen knife. According to the prosecution this was because it was on the inventory for Sollecito's apartment and therefore if they disposed of it they would have had to replace it.
The defence theory:
The forensic evidence places two people at the scene of the murder - Guede and Kercher. There is no forensic evidence placing anyone else at the scene. Guede murdered Kercher. The bloody footprint on the bathmat is a problem since it appears to be Sollecito's and, even if it is Guede's, no credible mechanism for its presence has been presented. But, as already highlighted, this footprint is a problem for the prosecution as well.