I'm a huge fan of Coyote swap. The comparible cost completely over looks the value of your time though. A Coyote swap takes real time, where a crate motor is a drop in with a far lower time investment. Some people make cost suggestions without the understanding of how much free time different people have. Congrats on choosing a crate engine; I have lost many hours of my life coordinating with machine shops, and getting parts where they need to go. There is a lot to be said for swiping your card, and the complete engine shows up truck freight days later. I also have grown to like the Ford parts too. There are better heads out there, but nothing seems to fit and work as well as the parts that Ford makes.
I would consider swapping those valve covers for the Trick Flow valve covers. Unfortunately, Ford is still too focused on old hot rods with carbs, and doesn't offer a low profile valve cover. The Trick Flow ones are designed to work with a fuel injected engine, and will be without a doubt the best step towards getting more clearance for your stock hood. It was the best investment in clearance I ever made. You can also put a real filler neck on it.
I would also look at the BBK headers over the Kooks. I doubt there will be much performance difference between the 1 7/8" over the 1 3/4", and the BBKs fit so much better, and less than half the cost.
Kurt