I am having problems with misfires only on drivers side at RPMs over 5000. Dealership shows misfire codes, secondary cat readings seem to be OK and similar to each other. Having trouble diagnosing problem.

My '04 S4 with 85,000 miles has been starting somewhat hard, has to be pushed very hard to get over 5000 or so RPMs, gets misfires on 5,6,7,8 but only at high RPM while pushing harder on the accelerator. MIL flashes for a moment when this happens, then light stays off until you try to push high RPMs again. Misfires are more on 6, and 8, but all on drivers side. Passenger side is fine. My gut tells me bad cat. Any ideas? I did have a coil problem with 5 and 8 in January and the exhaust smelled bad, too rich at that time. Light was flashing at that time. Replaced all 8 coils, its been fine until now. Could I have cooked cats and took til now to see it?

I am tempted to replace entire exhaust with APR, but hate to spent the money if it will not fix my problem. Please help!

 

If you're not getting codes for the CAT, I wouldn't replace it.
Pull spark plugs from the missing cylinders and read them.

 

I'll second the cat, if the cat is "ok" then change the EGT sensor.

If you are getting the misfires on both banks, clean out the MAF.