[84LX89GT]

Over time header flanges warp and sometimes will develop chronic leaks from the gasket area. I've had the same headers for four years and two different mustangs and they still seal fine even with cheap gaskets. It all depends on the thickness of the header flanges and how much they warp.
If you want a dual exhaust system what i would do is buy everything that you want most because you'll have to listen to it every time you're in your car, so find the mufflers that sound best to you. You'll also have to probably buy a hanger kit to convert it to GT exhaust or have an exhaust shop install their own hangers.
The stock tubular manifolds (headers) on V6's aren't that bad and seal reliably although if you really feel like it you can buy aftermarket headers.
If i were you i would skip on the headers, buy a quality H-pipe or X-pipe and get the cat-back system you want, that way there's no compramises. It would work fine having an exhaust shop fabricate a custom exhaust using the old exhaust as well, it's all up to what you prefer.