As I alluded to over in the "dyno" section, headers take the Contour out of STS because of the precats. STS allows headers, but they don't allow removal or alteration of any emissions equipment (cats).
There is no direct rule on the Y-pipe. Most of us have surmised that it's legal based on interpretation of the rules. Stock class allows the cat-back. STS allows headers for everyone else, which opens the door (by extrapolation) for mods in front of the main cat. The Y-pipe does not remove or disable any emissions equipment. Voila!
Intake is fine, but the MAF is also off limits. No reason to change it, anyway.
Brakes have to be the same size and type as standard, and stock calipers must be retained. Slotted or cross-drilled are legal, but I wouldn't recommend them. No fancy modular rotors or lightweight fixed calipers allowed.
As for priorities, IMMHO, I'd do tires before anything else, even if weight reduction is free. Somebody seasoned on nationals events put ergonomics next, even ahead of suspension. That's harness/strap/whatever-it-takes-to-hold-you-in-the-seat, "race" pedals, good helmet, etc. Everyone has their own ideas, though, and that's good.
