"What about AK knowing the manner of MK's death before the results of the autopsy had been made public"
several people were in the house when the door was broken down, infact it was one of the housemate's friends who knocked it down and he (and at least one other person) saw the policeman enter the room and lift the duvet away from her face.
Any of those many people could have talked about what they saw and so it's not surprising that Knox would be aware of speculation about how she died or where she was found. Infact, Knox said meredith was 'in the wardrobe' when she wasn't. She didn't know but she was aware.
Multiple assailants theory has been challenged.
The woman who heard the scream didn't come forward immediately and when she did I believe she went to the press first. Hearing people running is circumstantial evidence and can't be proven to have been the accused.
There is evidence that there was a clean up? I think there is evidence that some areas were cleaned, it is entirely possible that this was Guede.
Staged burglary, if that's what it was, could also have been Guede. Although it could have actually been a break-in.
"What about the fact that they lied about having called the police before they arrived (as confirmed by CCTV, phone records and RS himself)? Inspector Battistelli testified that Amanda Knox and Raffaele Sollecito looked ?embarrassed and surprised? when the officers found them standing outside the cottage."
not been proven beyond reasonable doubt. Teh CCTV footage shows the police car in a certain place at a certain time but doesn't prove the police got to the house when they say they did. Human error happened when logging times at least once. Battistelli said they were hugging and looked embarrassed and surprised. He also said he didn't enter the room after the door had been broken but two witnesses testified that he did.
"What about AK knowing where Meredith had been murdered (which was not the same place as where her body was found)?"
what do you mean by this?
"What about AK's blood, mixed with Meredith's being found in the bathroom they shared (none of Guede's DNA was found in that bathroom)?"
are you sure. It was AK's blood, really? I thought it was her DNA which was not unusual as she had been a frequent user of that bathroom. I think the Truejustice site are still claiming it is blood but this is not accurate.
"What about Amanda's footprints, set in Merediths' blood, found in two places in the hallway of the new wing of Meredith?s house. One print was exiting her own room, and one print was outside Meredith?s room, facing into the room. These bloody footprints were only revealed under luminol."
these were not bloody footprints. They were partial footprints some with some spot traces of meredith's blood, some without. The blood could have been transfered from the bathmat when AK left the bathroom after showering. Although none of the other people who lived there were checked against the footprints. They could also have been old footprints and Luminol reacts with several other things, not just blood.
"What about a woman?s bloody shoeprint which matched AK?s foot size, found on a pillow under Meredith?s body?"
this was a partial footprint which the prosecution say could be the same size as Amanda Knox but they were unable to prove that it was a print of any of AK's shoes and infact it had patterns the same as the other footprint which they first tried to claim was Sollecito's but then proved was Guedes because it was a match for his shoes. The sizing of this second footprint may not be accurate as it was only a partial print. Most likely it was just another print from Guede.
"What about the knide, found in RS's kitchen, with Meredith's DNA on the tip, and AK's on the handle?"
the DNA trace was not conclusive and this evidence is seriously flawed. see here for the science bit
"What about evidence that this knfe had been scrubbed with bleach? "
as far as I am aware the police said they could smell bleach and so assumed that the knife had been cleaned with bleach.
"What about the mixture of Knox?s DNA and Meredith?s blood that was found in Filomena?s room? Yet AK never claimed that she entered Filomena?s room when she checked the cottage."
did she ever go in that room, they lived together and so I am sure she did at some point.
have not answered all your questions but most of the things asked have been discussed at great length in the thread at some point.