Okay, so, obviously a lot of disagreement here.

Regarding the base rate of contamination, the first thing to remember is that in the case of the knife we're dealing with a Low Copy Number (LCN) sample, for which the risk of contamination is greatly increased unless extremely stringent protocols are followed -- protocols which were not followed here. So we're probably talking about an order of magnitude increase in the base rate: more like 1/5 instead of 1/50.

(Incidentally, there was never any "first independent report" prior to this one: the defense's request for an independent review during the first trial was rejected. What you are most likely referring to is the fact that Stefanoni's own bosses at the Polizia Scientifica signed off on her work, well before the trial. Based on what's in the Conti-Vecchiotti report I consider it likely that they didn't scrutinize it very carefully.)

Secondly, thanks to Conti and Vecchiotti, we have considerable Inside View information about the reliability of this sample in particular. And there's every reason to believe this result is completely bogus. Indeed, Conti and Vecchiotti come pretty close to accusing Stefanoni of outright scientific fraud. Here are some of their observations:

• The sample in question (Trace B) tested negative for blood, as did every other sample taken from the blade. (Samples from the handle were not tested for blood.) No attempt was made to scientifically determine the actual nature of the alleged biological material.

• When "quantification" (test to determine whether there was enough DNA to be analyzed) was performed, Traces B and C both yielded a result of "too low". Stefanoni reported Trace B as a positive result, and Trace C as a negative result, without any justification. There is no documentation in the lab data to support her statement in court that the Trace B sample was in the range of several hundred picograms. Stefanoni also claimed to have executed steps in the quantification procedure that are not documented.

• The "amplification" (chemical copying of the sample in order to produce a large enough amount for analysis) was performed only once, despite the fact (admitted by Stefanoni) that it should be repeated in order to be considered reliable.

• Stefanoni did not perform negative controls, which could have indicated the presence of contamination.

• The sample was analyzed in the same laboratory at the same time as numerous samples containing Meredith Kercher's DNA.

In short, everything smacks of a deliberate effort to obtain a certain result -- which was obtained easily enough given the lax procedural standards and absence of safeguards. I thus have very little hesitation in dismissing the knife DNA.

Now, regarding the "circumstantial evidence surrounding the knife" that you listed, I see two major general issues. One is that you are misinformed about a number of details, apparently as a result of uncritically accepting claims from pro-guilt sources (cf. the "first independent report" misconception above). You should be extremely skeptical of pro-guilt advocacy sites such as PMF or True Justice -- they are caught up in a death spiral of hate and constitute an absolute breeding ground of anti-epistemology the likes of which are usually only seen in political or religious conflicts. No, that doesn't mean everything they say is false, and yes, the pro-innocence community is vulnerable to the same disease, but in general I would advise against assuming any claim of theirs is true unless it is explicitly conceded by the other side. For example, this is wrong:

The knife was on top of the other knives, and matched one of the murder weapons

In actuality, the hypothesis of more than one murder weapon was invented specifically to accommodate the fact that this particular knife -- which investigators had already decided was the murder weapon based on "police intuition" followed by the bogus DNA result discussed above -- turned out not to match certain wounds on the victim, nor an imprint found in a bedsheet; a clear instance of motivated cognition and -- given that a smaller knife would have been compatible with all of the wounds as well as the imprint -- a patent violation of Occam's Razor. Another claim without any foundation is:

The same knife was bleached, and the other knives weren't

The closest thing to evidence for this is that a police officer claimed to have smelled bleach upon opening the drawer that the knife was in. (That doesn't distinguish the knife in question from the others, needless to say.)

The other major issue is that in my opinion you wildly overestimate the evidentiary strength of the observations that are true. This applies to all of items 3 through 6. For example, I see no reason why Raffaele's claim about Meredith visiting his house should even have a likelihood ratio as high as 2, let alone 100. The innocent explanation is that he had been told about the knife DNA result, and believed it. Given that he didn't have the Conti-Vecchiotti report available, why do you consider the likelihood of this to be only 1/100 that of a corresponding guilty scenario? Similarly, why is Amanda's reaction to the knife drawer even evidence of guilt at all, let alone 10 decibels' worth?

Item 5 seems to me to be another example of overconfidence:

Where Amanda's DNA was found on the handle suggests someone stabbing rather than cooking with it: meh, shift by 2.

Even if this is so (which I don't have any particular reason to accept), presumably all one has to do to to get one's DNA in this position is shift one's grip on the knife in some way -- as opposed to actually stabbing someone! Isn't the denominator of this ratio quite substantial?

Amanda wrote in her diary speculating whether Raffaele may have framed her by pressing the knife in her hand while she slept: Shift by 10, this is not something you'd write if you knew the knife isn't a murder weapon.

But in this situation "knowing the knife isn't a murder weapon" doesn't come close to being necessary for innocence. She knew that Raffaele was a suspect along with her, knew that Meredith had been killed with a knife, and (depending on the chronology) may have known that Raffaele's knife was considered the murder weapon by the police. Under those assumptions, it's an entirely natural speculation, it seems to me.

Also, here is Amanda's quote in context:

So unless Raffaele decided to get up after I fell asleep, grabbed said knife, went over to my house, used it to kill Meredith, came home, cleaned the blood off, rubbed my fingerprints all over it, put it away, then tucked himself back into bed, and then pretended really well the next couple of days, well, I just highly doubt all of that.