RF,
The Ford Racing muffler is a ton quieter than the Stainless Works headers you have now. It would require quite a bit of cutting and fabricating to join your current headers to the Ford Racing muffler however. A better solution, especially if you do not want to use catalytic converters, would be to sell your Stainless Works header system intact and purchase the Ford Racing headers that are designed to hook up to either the stock muffler or the Ford Racing muffler. I am not talking about the rear exit Ford Racing headers that are incredibly loud, but the other headers that Ford Racing offered that hook directly up to the muffler and do not contain catalytic converters. I realize that they are no longer produced but you may be able to find a set somewhere. Again, Jack at Muscle Motors would be a good source here. Many of us who have heard that set up think it is the best sounding Ford GT exhaust system that exists. It is has a deep, just loud enough, excellent sounding tone that is calm at low throttle settings and roars like a tiger at full throttle. That is the direction I suggest you go in as it would be quieter and more pleasant during low throttle driving than your current system. All the best.
Chip