Raptor's headers are not direct bolt-on. The stock midpipe needs to be cut, an step up adapter needs to be attached to the midpipe, and then the adapter needs to be welded to the pipe and the provided flanges. However, I don't recommend that you do it that way because the increased exhaust pressure from the headers will destroy stock cats.... It happened to me, it happened to perscitus, I'm sure it's happened to other members (That's all in this thread). Not to mention the fact that the stock section of pipe is thinner than the outlet pipe on the headers.
I would recommend you price out a pair of high flow cats, I used Vibrants, and I believe Perscitus did as well, and plan on having a midpipe fabricated when you do it. I paid around $1200 for my midpipe fabrication including parts using stainless tubing. I'd recommend you shop the project around a bit to your local speed shops. Show them pictures of perscitus's midpipe.