Replaced spark plugs,
next guess is coils, then injectors
Your ignition coils are not included in the service action mentioned by some other answerers. Your 2.8 uses waste spark ignition, which uses one coil to run two cylinders. When a coil goes in this type of setup, it’s fairly easy to diagnose. You can trace the plug wires to the coils that run them. I can’t remember which coils run which cylinders, but I do know that each coil runs a cylinder on each bank. If a coil fails, then the two cylinders it runs will have a dead miss. Another cylinder or cylinders can misfire as a result of the slow-down of the crankshaft, but they will be more random. I would consider replacing the wires before replacing a coil. They undergo a lot of heat cycling and can be prone to failure. I would definitely be checking mass airflow and vacuum/pcv. Try disconnecting the mass airflow sensor while the vehicle is idling. Keep in mind that any major vacuum leaks need to be taken care of first. If the engine runs smoother with it disconnected, you may have just found your problem. Good luck!
Ignition coils! Had same problem with mine a fee yrs back. Luckily, it was replaces under warranty- you should call Audi and check if they’d honor this recall (there was a recall on coils… But they wouldn’t replace unless they failed). Good luck!
Coil is a common problem and most likely your problem. It could also be a vacuum leak. Check and make sure that all hoses are hocked up and no lose clamps or holes.
Before you drive yourself nuts, the usual cause is DIRTY IDLE AIR CONTROL VALVE. second most common cause is, CRANKCASE VENTILATION HOSE. Third cause is DIRTY THROTTLE BODY. $10 in Gum-out spray usually cures most of this. POWER WASH your engine to see things more clearly. Hopefully, you are using a fine plug like a Denso Iridium or Bosch Fusion plug. The newer Denso Twin Tip plug is awesome. Check your PCV hoses for breakage. They get very brittle over time. REALIZE THAT your engine MUST have a special oil used in it, since it has PISTON SQUIRTERS built into it. NO VALVOLINE!! Oil must meet specification 502/505. This meas Mobil One, ELF, Pennzoil Ultra, and German Castrol. NOTHING ELSE. The correct oil will have the name “AUDI” printed right on it, as in “engineered for use in AUDI products.” SEE??
I’d check for an intake manifold leak first. Sure is a lot cheaper to test than randomly replace!