Its considered a modification because it differs from what the factory supplied. Regardless that the dealer installed it.
No one's going to say anything about the sho-shop y-pipe, the power difference is insignificant and as Matt mentioned the Contour as it stands isn't competitive enough. We'll see next year though. The headers as noted above are illegal. (don't think I ever claimed they were..)
I don't see why the shifter mod should even be mentioned, in the Solo II events you don't shift so what difference does it make?
Rather than changing the shifter I'd move to straight cut gears to allow for clutchless shifting under power... Now that would make a difference.
The LSD is really the Mod that's needed for contour but that moves you to one of the prepared categories, which is a lot more mods than just that one.