How are you validating that the MAF is good? You're using a filter with less filtering capabilities than a paper element, so your MAF probably needs a good cleaning. Easy enough to do.
Also, you probably have crud built up at the throttle body. Being DBW, if you ever reset the battery, it will lose it's calibration for the buildup, and give a wonky throttle position.
Finally, check out your o2 sensor, and replace if needed.
All of those things can lead to weird readings and poor performance.