Update 4/4/2013: I received a private message from Bronson@APR today. I was told that the MOFSET chip on my ECM was fried. He said that this was something that happens to ECM's that have an -AT suffix and is not a poor installation/software issue.
Unfortunately, that leaves me in a very poor financial situation as I spoke with the service manager (Todd Ellis) over at Emich VW and was told that even if the issue was OEM related that he could not warranty the claim based on the aftermarket software alone.
So, this is where we stand now... I am told that this issue is OEM related and something that was not caused by myself, APR's software or Avalon Motorsports' installation. However, I still have a looming repair bill sitting over my head and the manufacturer (VW) will not touch it based on the circumstance. As such, I am currently waiting to hear back from APR to see if they will at least assist me in good faith since this issue occurred through no fault of my own and would have been warrantied otherwise. I will keep you guys posted.
Not that it matters much, but here's a pic of the damaged ECM that I received from APR: