Mufflers first, then x-pipe. Generic mufflers usually don't sound as good on cars with catless headers and s-pipes. The cats hide a lot of the rasp and resonance... once you get rid of them, it a tuned system becomes more important.
I have a video of catless headers, resonated s-pipe, and Stromung mufflers. If you're interested, I can ask the car's owner to post it. I think RatedM had this setup too, so you might check out some of his videos.
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