I've had the cowl-flap noise on my 2010 Ford Taurus. Kind of a buzzing sound. Not sure if the Explorer is the same, but the cowl on the Taurus is a softer plastic and, if stretched even a little, can be loose enough to vibrate at highway speeds. Ford replaced, but it could be a problem again later.
Have seen fit/finish issue on an 2011 Explorer in our parking lot. Hood is clearly misaligned and actually sits off-kilter. Not by a lot, but noticable. Agree with earlier poster. Unit should never have left factory. If my untrained eye can see it, the factory should have.
Awaiting my 300A Limited in Ingot Silver. Ordered 1/5. Due to be built 1/31. ETA 2/14. Based on comments here, that seems optimistic!