Check the intake manifold.I own a 05 a4 3.2 quattro had almost exact same problem,went to several audi dealers and local shops,i was told everything from my transmission was bad to my computer had failed,the final audi dealer found the problem first try.CRAPPY GAS !!!HAD CAUSED A HUGE CARBON BUILDUP ON THE INTAKE HAD TO CLEAN IT COST 700 BUCKS --RUNS LIKE NEW!!! WHEN I SAY CRAPPY GAS I MEAN EXXON,BP,TEXACO,AMOCO---ONLY USE CHEVRON OR SHELL GAS----ONLY!YOU WILL BE PLAUGED WITH PROBLEMS IF YOU DONT!!!!pull the plastic intake all the way to the manifold-top of engine-look inside is it black and sooty on the aluminum intake and valve?at all?if yes there lies a major problem-if you used low quality gas for too long the valves WILL need replacing also 1200 bucks-or more along with the 700 for cleaning.I WOULD START HERE IF ITS DIRTY AT ALL YOU NEED TO PULL OF THE TOP OF THE ENGINE AND SCRUB THE INTAKE MANIFOLD AND THE VALVES GOOD.this buildup will cause single cylinder misfires-multiple misfires-rough idle-bad hesitation-hard shifting-and much more.audi engines are very precise machines and need to be treated as such by only using what we call TOP TIER gasoline-shell,chevron