I took my list and car to Double J Motorwerks in Portland. They did a great job putting the below together in very quick time:
2012 GLI: Volkswagen Racing Intake/Induktion Motorsports pipe. APR Stage III K04 kit, S3 FMIC, Techtonics Tuning 2.5" downpipe, Techtonics Tuning 2.5" Dual Borla exhaust, H&R Springs
Joey took great care to make sure everything was right. We ran the car a few times and noticed some misfires. After agreeing to take it easy on the car I took it home for the weekend where I experienced more misfires, all the way to the point of disabled cylinders.
It was suggested that the plugs be regapped; still problems.
Swap plugs with $13 a piece NGKs; no change.
The hardware is all VW/Audi, and the engine has only 1600 miles on it so it's not a hardware issue. We know there's plenty of air and compression so that leaves just fuel or spark as the culprit. It runs ok at lower RPMs with random single misfires, but under load or above about 4k bad things start to happen.
It seems to me that the software isn't figure out quite yet. I'm royally disappointed; I chose APR because they are a world dominate programmer for VW/Audi. They have been alerted to the problem, so the ball is in their court now. We'll see if APR remembers the Volk in Volkswagen.
Thanks to Josh at TT for the quick exhaust build and Joey and the team at DJM for transforming my car so quickly.