I call up my friend Erik that owns I.P.M. Auto Service here in Redmond and ask him if he could bring the Vag-com over. After a quick scan it showed that cylinder 6 was the only one misfiring. We took out the spark plug and it looked just fine. So we swapped in a old OEM coil pack that I had kept just in case. Fired up the S4 and it was running fine. First time I was able to get something fixed in under a hour and at no cost.
What's odd is that all of my coil packs were replaced 2 years ago/30,000 miles so they are not old at all. They are the Beru brand so maybe the quality is not that great. Hopefully the rest of them are ok and stay that way for a while.