It's funny you say you want a more modern sound, because most of the late-model guys want an old-school sound to their Cobras. Personally, I think each is great in their own way. And in reality, it'll be impossible to get that close to a modular overhead cam sound.
If you want to get a modern sound (at least as close to the late-model sound as you can get), go with
Borla and some type of intermediate x-pipe (
Borla doesn't make them, but Magnaflow and Bassani both do).
Borla and Bassani (also good imo, but I like the T-304 stainless
Borla uses as opposed to Bassani's lower-grade 409) are two of the more popular late-model aftermarket manufacturers. Both will deliver a nice, aggressive, throaty sound in a much more refined manner than Flowmasters.
And keep in mind when I say
Borla, I'm excluding the XR-1s. These can be very loud, poppy, raspy, etc and great for what they are (I chose these for my '98 Cobra and '65 Fastback), but I don't think these are what you're looking for. I think
Borla XSs will deliver exactly what you seem to want.