I think that 2002 A6 might be BEL engine, you'd have to double check that. If it is BEL, you'd have to do some extra work (like swap knock sensors) before it would work in S4.
The earlier S4 (before '01.5) had EGTs mounted on separate sides of the motor, as opposed to the A6 that has them mounted directly on top of each other, and the IM is diff. Also, you'll need to block off the SAI ports on the back of the motor, if you're hooking it up to a manual.
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