I pulled the radio, and it's turns out that the fuse on the back of the radio had blown. So for future reference, there is a fuse back there, and if it blows you lose the ability to connect to the car with vag-com. It is a brown 7.5amp fuse for those who are interested. I replaced it, and now it works fine (so far). I need to find out if there is something else wrong with the car that caused the short.

UPDATE: The short was in the CD changer.

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*I am not a mechanic nor an expert in Audi repair/tuning. In no way are my posts meant to replace professional consultation.*