Ok, two things jumped out at me right away. One is major, the other is more aesthetics than anything. The minor one is the breather from the drivers valve cover to the intake is backwards. Very minor.
The major one is the ground at the front of the passenger side of the valve cover. This may be what is causing your issues. I can tell from this ground that your car is either a late '11 or '12 5.0. Unfortunately the Whipple kits do not account for this change with the FEAD bracketry. What I do to secure the ground is to drill out the o ring terminal a little and secure it under the head of the bolt on the timing chain cover.
I've reattached your pic with the 2 items circled in red. Get the wire grounded and let me know how you make out from there.