First off, i'd put the Neddwings CAI back on. I can't think off anything that would cause this, except some kind of air or vaccuum leak. This usually causes surges, rough idle, etc. I think this maybe gave about 3-5 HP increse, but the biggest change was the sound of the engine. I remember taking the Air cleaner off so we could hear the carb honk on my old cars as a kid, that is what this sounds like.

I would check at the MAF where the sensor is mounted for a very small vacuum leak. Is is possible that the Elbow body cracked where the the baffles were removed?

Sorry ,no other ideas.