I had the same problem last spring when i purchased a FMF ti powrecore muffler. I removed the header pipe from the bike in an effort to make it fit. It was an impossibly tight fit as well. I phoned FMF help line and the guy seemed suprised to hear this. He suggessted cutting a slot in the muffler. I wasnt to keen on this. I took the header and pipe to the muffler shop down the steet. The owner put the head pipe on his tube bender and expanded the opening just the right size to be a tight slip fit. Mounted on the bike perfectly and no charge from the muffler guy.
P.S. the muffler works great. Good value for the money