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You said, "....obvious that the rotors were the cause of the wobble." Although it may happen under braking, the rotors may be in good shape. There's a decent chance their are pad deposits on the rotors, causing unequal friction as the disc rotates along the pad. Try re-bedding the pads an see if that cleans it up. To do this, threshold brake 5-7 times from 80 mph to 20 mph or so. This will heat up the rotors and clean off any potential deposits. Your brakes may smoke after this, but don't worry about it if they do. Try driving without using the brakes at all for about five minutes after doing this to allow the brakes to cool evenly.
Also, what kind of pads are you using?
Be sure not to use the parking brake when the rotors are very hot.
Disclaimer: I'm new to the Boxster scene, so my comments are based on Audi experience, which is significant.
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