When I had an intake, my car's ECU stop downshifting into the most optimal gear. For instance, if I was going 60 and I floored it, it'd shift into 3rd and not 2nd. With the intake off, now it shifts fine again. So my question is, will a y-pipe possibly have the same effect?

I don't think it will, because it's exhausted air, and not taken in air - so the ECU won't make any sort of adjustments anywhere. But still, I figured asking couldn't hurt.

 

Mine does not shift down to 2nd most of the time when cruising at 60 and flooring it from steady speed, although if I drop the gas pedal and then quickly floor it, it will shift into 2nd sometimes... If I need to manouver instantly, I will manually put in 2nd... I don't recall how it was before Y and intake, it was so looooong ago