If you do a custom anything on the exhuast, get the intake on there first. The place I went to said they can adjust tone to be sure I don't get that annoying snapping sound. My neighbor's F150 does it everytime, and I clench my teeth at the cheap and horrible sounding pipes he put on.
And from my searching, I would go to a custom shop, price is a bit better than bolt-on and you know it will work the way you want it to when they are done.