ahh, the B6 S4 Type 8E2 the 4 door, or the 8E5 the avant version.
there are many common problems. the main being electrical. But i got this from a forum that i frequent alot. Its a huge thread, but everything you want to know about the B6 S4 is on their. From problems to DIY fixes to proper Dealer fixes. Hope this help.
Common Problems & Mechanical-Electrical Differences of the B6/B7 S4
Common trouble codes or Engine Electrical problems. and solutions
-Code = 18613 - Performance Malfunction in Cooling System
P2181 - 008 - Implausible Signal
Solution = If your coolant sensor checks out ok or has been replaced and your car is full of coolant this is MOST likely a sticky thermostat. (We sell these)
-MAF (Mass Airflow) sensor issues or MAF codes. These cars have Bosch MAFs which are notoriously known for the HIGHER than normal failure rate. We have seen this in the early B5 S4, B6/B7 S4, Jettas, A4s and many others. So MOST of the time if you have MAF codes or if you get weird long term fuel trim codes that are not due to a bad 02 sensor then it is highly likely your MAF is bad. (We sell the replacement electronic portion for a low cost on our site.)
-Missfires (shuttering or rough running engine) or flashing CEL. The CEL flashes to warn you that your car is missfiring and you WILL damage your catalytic converters if you don't fix the problem. Most of the time this is one or some of your coil packs going bad. The coil packs (8 per car) have been updated by Audi for the B6 and the B7 S4 several times and they are currently on revision Q. This indicates they are aware of this problem. (We sell the replacement OEM updated Q coil packs on our site.)