I've put a lot of thought into a header and exhaust system myself. Now I'm not sure what you want to do, and since you're in salty territory, you might want to go with SS piping and mufflers. That puts a bummer of a spin on things because I have YET to find a SS glasspack at the usual parts suppliers. Anyway, I'll run through some of this for you so maybe it will help you out.
First off, I'm not too big on removing cats without replacing cats in road vehicles. I have my reasons- knowing the air quality in Alaska while in Hong Kong on a windless day gave me reason to think. That being said, it's hard to find a good cat that isn't going to cause some blockage of some sort.
There are high-flow cats that aren't CARB approved, but will do something. Dynamax makes one in every exhaust size for $160 from Summit. I wouldn't put a system together without everything being the same size and number, so two of those would be needed behind the header. Flex pipes are a good idea also to reduce road vibration strains on header's gaskets. Resonators are basically glasspacks, but hard to find in SS. I do not know for sure, but Tru-Bendz advertises an add on resonator with their systems for $60. It would be worthwhile to ask them if it came in SS. Now comes the muffler problem. Not much fits in the space where the Focus muffler is mounted on a Duratec. I did find a Magnaflow 3 chamber muffler that would fit, and should be a quieter choice than the standard Magnaflow. It took some reading, but Summit sells it too. If it's still not quiet enough, you can always use a resonated tip.
You might want to do some measuring behind the rear wheels also. In a wagon, I can fit a Flowmaster 50 Delta2 after the rear wheels. I'm not sure how much space is behind the rear wheels of a sedan so you're on your own measuring that. A 60 Delta would be a good muffler and is made for sport compacts, but only comes in 2.25. I wouldn't go with a 40, some of the new ones might be better sounding, but the older 40's were loud and without the benefits of larger FM's.
I hope I helped, but basically I think the only way to keep a Duratec somewhat quiet (depending on your opinion of quiet) with a header is put some kind of muffler or resonator in every available place in the exhaust system. I'd try to stick with high flow mufflers all around, like the Flowmasters and glasspacks. There are even some better mufflers out there to consider, but not many that fit in the stock location. Gibson mufflers, for example, won't fit ANYWHERE and neither will Dynomax because they are so large. There are also spiral type mufflers that can be small in size and could be used as resonators, and I think a company named Pro-Flo makes some in SS.
Best of luck [thumb]