I'm definitely considering an AEM. However, I'd hate to buy one and then have it still miss. Plus, I understand its a bitch to tune and you need a laptop for tuning. I don't have a laptop (although I suppose I could buy an old one) and I hate the idea of having to tune with a laptop... just not convenient.
As far as this air flow issue causing the miss, I don't think the two things are related. I did some more driving around and while driving in 1st and 2nd gears and the AF signal shows a smooth transition even though it misses. It seems that the aberrations in air flow signal only seem to come on in 3rd, 4th and 5th gears. I think this may be the "pressure pulsing at part throttle" problem talked about here:
Pressure Pulsing at Part Throttle, Measurements and a Solution