The cell phone evidence and the changing stories are what gives me reason to a probability of guilty to S and K above .05. (See my comment for my probabilities). The effect of this evidence was mitigated for me by:

1. Their likely intoxication during this period.
2. Police coercion leading to confusion about the events.
3. It looks like a lot of what the pro-guilty site claims ended up being unproven rumors not produced in trial, this makes it very unclear to me what story S and K actually ended up giving in trial. Since the site exaggerates other claims their claims about the cell phones and the stories can't be fully trusted.

You weren't troubled by the lack of motive and the fact that after covering up her involvement in a crime but intentionally leaving evidence of Guede's presence Knox went on to point the finger at someone who couldn't have been involved after being coerced by the police? Shoot, I can't figure out why Knox, if she was guilty, wouldn't have just stayed at Sollecito's until someone else discovered the body.