By making stage 3 active you may be adding a lot of OpAmp noise, since you're amplifying it by a factor of 100 at low frequencies. It sits behind the first two gain stages so it might not matter for the input referred noise? But I don't think it's good practice. What was wrong with having that stage passive? A gain stage like this, which doesn't provide gains higher than 1 and actually attenuates over a broad range is usually better kept passive because of amplifier noise.

Did you check the circuit for stability? The AD829 in stage 3 is driving a pretty low resistance as load. Not sure if LTSpice can identify such problems.