I have done a fair bit of research about the 2 way and 3 way ACIS systems and i happen to find that if you are running n/a do not pull a toysrme and remove it (turbo i would follow his lead for sure).
Toyota put that in for a reason and that is to help midrange and i would like to say high range but when i say high i mean upto like 6000rpm
When you have the flap OPEN it turns your intake manifold into a short runner plenum intake setup. You now have about a 9" runner intake manifold (not including the lower plenum). This helps you with "upper" rpm range and is generally what you want for turbos as well, however this lowers torque numbers in the lower end and the get up and go power is lost (where you loose your time on the track).
Now when the valve is closed you now have a 15" runner intake setup with the left and right bank having there own mini plenum at the 9" mark, but since 1 intake valve is pretty much open at a time on each bank its safe to say you have ONE 15" runner per cyl.
LONGER intake runners help with your get up and go torque...(this is why the 5vz has a 26" long intake runner setup :O) if anything i would have the low end torque setup on all the time (which you did) as at that point you will see gains.
If you are dragging and never see below roughly 4500rpm then having it open is the better way to go.
The 3mz dual TB intake manifold helps this even more because now you have a 3 way adjustable intake system which will help the bottom end even more as each bank get their own TB.