He called MF at 12:14PM. This is what points to innocence in my opinion. If he's worried about his 2 year old left alone all night, why not call MF first thing in the morning to tell her to go get the print-outs?
I agree that initially, I also believed that sending her to the house for the print-outs seemed suspicious but after learning more about the case and hearing about how he and Meredith had been in fairly regular recent contact as she was playing marriage counselor, it seemed normal that he would call and ask her to go retrieve that. He was trying to please MF and Linda by buying her an anniversary gift. He knew they were upset with him because he didn't buy her a gift.
I believe MY would have been expected home late that afternoon - 4-5PM or so.
What if JY hadn't been able to reach MF? He planned to spend the night in Brevard with family. At what point would he have begun to worry that he couldn't reach MY and had to drive home? I just don't understand why he would have worked the overnight trip in Brevard into the plan. Why not go home after the meetings to ensure he would be there for C. (just in case he couldn't reach MF)
Also, if he's responsible for the murder, why would his first call that morning be placed to his mistress? Wouldn't he have been avoiding her, knowing they would be checking his phone records? In fact, he had called her so many times in the weeks prior to this and would have known that would be a red flag. Everyone knows now that the spouse always takes the fall for a murdered spouse - evidence or not, alibi or not, affair or not.