Man, I wish I could get my wife interested in autocrossing. That would be frickin' awesome (and sexy as hell)!
As an amateur autocrosser (Champaign County Sports Car Club) in a Passat ('99 1.8T tiptronic), I'd say start her off in G-Stock (though it maybe H-Stock next year). Let her get a feel for the car before you start throwing money into it. She may decide it's time for an upgrade

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A cat-back exhaust won't move you around in classes and may free up some upper-end power. Shocks will also let you stay in stock.
A chip for a V6 will not give you nearly as much as it will for a 1.8T but it also won't bump you into SM. Probably STS and if you're there you might as well go with springs and a rear sway.
Pulleys will also only put you into STS but some here really recommend against it.
I don't know for certain but I think that the spring rates for the wagons are higher than for sedans (makes sense with the wagons being heavier). They may work, but the rear will probably sit a little lower.
Exhaust system is probably the same between wagon and sedan, as are the brakes.