Does the JBA shorty header for the Zx2 fit the '99.5 and newer Zetec with VCT that was installed in the Contour ??

I don't know what the exhaust and cat look like for the earlier non-VCT engines in the Contour, but the later VCT engines might connect up and maintain emissions legality.

With this setup all you are going to see is some improvement of top end power by eleiminating restricted flow of the OEM log manifold.