I also realized I never answered your OP question.
I remember a few posts that hotly debated your question. One camp argued that the stock brakes, well maintained, are very capable for many drivers who have no intention of tracking the car. The other camp pointed out the strengths of each upgraded item (ss lines, pads and rotors), both individually and as a package. Both made great points.
I do not think it's worth the extra money. Good fluid and pads are my vote for starters, and upgraded lines if you really want them (stock S4 lines are not like a Buick's - they can perform just fine). I just don't think my brakes feel that much better than the two other B5's I have driven that were running stock brakes.
If you are going to track it often, or pound through the mountains 5x a month, start shopping used BBK's.
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