Again, you may not be hurting anything, but the fact that you have to reset your ECU to make the car run well is very telling.
Go visit your parents, do some laundry and get the intake. They probably want to see you.
Swap it back on and see how the car runs. If it doesn't change anything, then the issue is with your exhaust.
What exhaust do you have?
Do you still have the O2 sensor in, or did you plug something in its place? Cat or no cat?
Oh, the other funny thing with many intakes is that the cones actually have less surface area than the OE filter. I'm not sure, but I think the volume of the air cleaner box also acts kind of like a capacitor evening out the intake pulses...