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Since you refer to headers, I'll answer with respect to the application of aftermarket headers to different MY C5's. There are some differences in catalytic converter and pre-catalysts (pup cats) depending on the MY and model of C5.
The mount for the Air Injection Reaction (AIR) system which supplies fresh air during cold starts for emission purposes is different due to the change from fabricated stainless tube exhaust manifolds in the earlier model years to cast manifolds in the later years. You can see the small flange and tube welded to the #6 primary (2nd from rear) on my passenger side header in the pic below. This is the position for the later model C5. The earlier model has the AIR tube inlet welded to the rearmost primary.
Also, the earlier models have the threaded boss for the dipstick mount welded to the #6 primary while the later models have the dipstick mounted directly to the passenger-side head.