The Hooker Aerochambers are a straight through muffler, no baffles to restrict air flow. The Flowmaster 40's have baffles in the path of the exhaust.
I had the Hooker's on a '95 Bronco 5.0 with headers and 3" exhaust, they gave it a nice deep sound. I never heard them on a Mustang though.
I had Flowmaster 40's on a '84 Chevy Silverado with the 350, Hedman headers, and true 2.5" duals, no cats. They also gave that truck a mean sound as well, especially with the aggressive cam. But, then again that's no Mustang either.
All in all, I think the Aerochambers would allow for better exhaust flow.
I'm sure some of those hear with a classic Mustang could give you better sounding advice. Pun intended.
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