The reason for the color differences between your hood and the scoop is age. Paint fades over time, particularly when they arent well maintained or if they are single-stage. This will be most apparent on broad areas most exposed to the sun (i.e. your hood, roof, and trunk). Your car is just over six years old, meaning the sun has had six whole years to have its way with your paint job.
This will result in a slightly dulled, lighter finish. Meaning your scoop, being only a few days into its own paint job, will look slightly sharper/darker. Unfortunately, not much you can do unless you plan on repainting the whole car.
A good friend of mine heads up the body department at a local Ford dealer. I helped (or sort of watched

) him repaint his '92 5.0L 'stang, after which I asked him about the waxing/buffing. If you think about it, waxing is effectively sealing your paint against the outside elements. The same applies to the different compounds that give off gases in the paint. Waxing, etc, too early cam cause tiny bubbles to form in the top coat of your paint, because those gases cant escape. Now with the poly-silver, that may not be noticable, but his Mustang was black, so we needed the mirror finish.
He recommended waiting at least 30 days before a coat of wax is applied.
Its looking good though, cant wait to see it on the car.
Geoffrey