Specifically in response to number 3: I contend that it is easier to coerce a machine than a witness, that forged bits can be perfectly identical whereas forged letters might not.
Machines need to be held to different standards for different reasons. If we lend them a greater veracity than is appropriate, how unforgiving might such an error be?
We live in a world of statecraft through malware with Stuxnet, Flame and Duqu. We live in a world where international telecommunications companies enable global eavesdropping and interception at the carrier-grade level.
You cannot discount the idea that his entire machine might have been compromised all the way down to the firmware, to elicit highly specific programmable responses choreographed in real time. That much is is honestly unlikely, and unrealistic, but in theory, the possibility is there.
Consider that he may have been a useful idiot. A patsy. That he was framed, does the physical evidence and circumstantial evidence seal off that path of doubt? How advanced could the Silk Road's administrators actually be? Could they have crafted such malware, to root kit his laptop and lead investigators to a fall guy, and then temporarily close up shop if he goes down?
I don't think that's what happened, but when a laptop is a key piece of evidence that a case may hinge on, The first thing I think of is how much control I honestly have over my own laptop.
Fabricating bits is not the same as fabricating other evidence. Machines are different.
As for your points #1 and #2, yeah, I'll agree that those are valid points and that sounds pretty damning, and I'll give it up on those.