I took off my filter, cleaned/oiled it, cleaned the MAF, blew out the extension harness, put everything back together, and things are better but not perfect. Once I cleared learning it runs better, a week without codes and my car is no longer hesitating on throttle, but I'm still not happy with my AF Learning/Correct values, as they are still on the rich side. I am going to make some minor adjustments to where the filter sits to see if I can improve things a bit more.
My tuner originally installed this intake for me and it looks like they weren't 100% happy with its placement either, because they had drawn two lines on the pipe. Not putting a flange on the pipe so that we could nail placement every time is a huge design flaw with this Cobb intake. I would strongly recommend against this product.