Update:
So I went over the Flex today and found a couple things. First, the spark plugs were the newer style and looked good, but were gapped between .038 and .040. I went ahead and threw the Autolite XP5364's in (gapped at .030). The next thing I noticed was what I consider too much oil residue and pooling throughout the IC pipes. I saw a drop just before the throttle body and a bunch of residue there. I noticed some in the pipe coming off the rear turbo to the IC. When I pulled the inlet on the rear turbo it was pretty dry, I didn't bother with the outlet since it faces straight up. I pulled the inlet on the front turbo and it had some residue. I pulled the outlet on the front turbo and quite a bit of oil drizzled out. At this point I'm suspecting the CCV is sucking a good bit in. So I cleaned out what I could and put it back together.
So I fire up the car and drive around. I already notice more throttle response and it is just smoother. I hammer it a few times and it pulls harder. The DH shows that I'm solid at 20 degrees of timing with boost around 11.5psi at the top of the gears. Long high gear pulls show AFR starting and 11.7:1 in the beginning and it richens up all the way to 10.7:1 at the top of the gear where the boost is at its highest.
I was not able to get it to misfire, however I was able to get a couple random shudders here and there on my second drive. I was not monitoring knock (not sure which PID), but I'm sure that's what it is. The AFR seems stable, but the timing would drop from 19-20 to 10 (sometimes lower) for a couple seconds and then everything would recover. Based on that, I'm guessing that this is not a bad injector or plug / coil type issue as the problem would be consistent and not completely random. I'm guessing that the motor is sucking in some oil and if enough hits a cylinder at once it will cause detonation.
So at this point I'm going to get my catch can on the CCV, get some seafoam in the next gas tank, clean out the IC pipes the best I can, and seafoam the motor. I will keep an eye on things for the next couple weeks and see if oil is still pooling. If so, I will work on getting the dealer to replace the turbos using my powertrain warranty.