Mechanical is a taller top gear. Also a hotter thermostat. Some cars have 170 degree thermostat. Some engines like to run a little hotter and produce better numbers. As far as the Intake the stock one will be better for fuel economy. Reading from your posts you're more inclined towards performance than fuel economy so you might not get rid of that intake. My stock intake setup gave me 38-39mpg on the freeway. When I put an Injen intake my freeway number went down to 31mpg. So it might be hurting you more than you think.
What else...the apexi safc/vafc requires some dyno time and might not get you the results you want. I would advice getting a scanguage 2. You'll raise a couple mpg from that alone. I have been told people that have standalone ecu's only raise their mpg by 3. Might as well get yourself a scangauge 2 and put out the same if not better numbers and it's plug and play.
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