I missed the third part, but watched the first two, and never watched Serial. These are the kinds of cases like Making a Murderer that become so weighed down with all the evidence interpretations, years between the case and their re emergence, it's hard to hell what's what, esp. in documentary form.
I just can't think why this kid Jay would invent this insane story and tell it to the prosecutors, that's the number one question that points to his guilt, beyond everything else. Why would he do that? Is there any compelling motive for someone who was not really a suspect, and had no real motive, to provide a detailed statement about the person with the most obvious and relevant motive? Kids in high school do things like that, and think they can get away with it.