UPDATE on my CEL....
Changed out my coils and plugs, cleaned the MAF, and cleared the codes. It would be ok for a day, then turn back on the next day. NOW if I clear it, the CEL will turn on during the second start up (after driving several miles on the first startup).
The codes that are being thrown are always the following:
P301 - Cylinder 1 misfire
P302 - Cylinder 2 misfire
A random misfire code will also pop up with it.
At cold start, it is very apparent that there the cylinders are misfiring as I can hear "stutters" in the exhaust rumble. I've essentially already ruled out electrical issues (coils, plugs, MAF), so I'm willing to be that its air/fuel related.
Made an appointment at 034 Motorsports to do a carbon cleaning on Jan 29th. Before then, I'm going to take it to Winn VW to check out the fuel injectors to see if those are faulty. I believe VW extended the warranty on this part to 120k miles, to which I'm currently at 116k miles.