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Sounds like you're heading in the right direction, I'd replace both sides of the the connector, and any wiring that looks burnt too. I'm guessing the burnt looking insides are causing high resistance when you have more power going through it.
The S4 has a dedicated fan relay according to the wiring diagrams I have, although I don't where exactly this lives. I suspect it's next to the EFI relay on the side of the battery box.
It should be a Green&Black wire from the ECU, Green& Red to from the fusebox and Green&White feeding 12V to the fans. (MY2001, the '02 docs I have won't let me zoom on the wiring diagram)
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