You know what... we might be thinking too much on this subject. Try turning the MAF itself, it may not be facing the right direction to accurately sense the air speed, condition, and temperature.
Turn it around the piping or something first before you call it quits. It's forcing more air, but I don't think the intake is so great that you'll need a reflash.
If that fails, then it might be a good idea to ask Scion what their thoughts are on this subject.
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