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Affirmative.
In all honesty until you change your cam or add some other big airflow improvements I wouldn't suggest messing with the stock VE table. Improving on what the factory did is going to be a tall order unless you've got access to a load cell dyno. You can make global rich / lean adjustments by scaling your cylinder volume constant.
EDIT: Oh, and another possible cause for more air getting into the engine than the MAF is measuring is... vacuum leak?
Understood. I won't mess with the VE tables while in the stock configuration.
Vacuum leaks are much more influential under light load and the fuel trims are fine there. I've had the MAF sensor off the car for cleaning and the rubber boots look to be in very good condition so I doubt air is bypassing the MAF. If it were lean everywhere I might fiddle with the cylinder volume constant, but it's only above 40 kPa between 1000 and 2500 RPM that it seems to be lean. I'm going to go for a drive to see if cleaning the MAF had a positive effect.
Just to clarify, the cylinder volume constant only impacts the speed density calculations. I believe the MAF fueling calculation doesn't need to know anything but the injector constant.
Another idea just crossed my mind - has your MAF had the honeycomb removed (aka descreened)? That would throw the calibration off.
MAF screen is intact.
I was thinking about fuel pressure and checked the vacuum line to the regulator. But if the pressure were high at low load the PCM would have to pull fuel then rather than add fuel under load.