The next time you get a CEL, get the codes as drexplode suggested then put it in stock mode and take it to the dealer. Tell them the symptoms and give them the CEL codes. Have them check for cam lobe wear and fuel pump issues specifically. They don't check for these issues as part of regular maintenance but they are inherent problems on our cars and the symptoms are what you're describing. I bet you're getting poor gas mileage too...
http://www.audizine.com/forum/showthread.php?t=153392
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