It's more likely the factory Aero Kit than it is is actual GT3 bodywork. The 3.4 M96 is one of the weaker versions of the family, but if it's made it this far it's probably pretty sound. Only thing I would insist on would an IMS bearing upgrade.
As to it being an "upgrade" from an 03 S, I'd say no. To move up from your 03 S you're either going to want a 3.6 or 3.8 powered Carrera or a 987 Boxster S.
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Boxster S
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