How to apply high gain to filtered signal without shifting voltage level?
C29 should be removing the bias voltage from your input and since you’re running the op-amp on a single supply you should be seeing clipping of the negative half (with respect to the bias). In my mind, the easiest way to get a consistent bias at the output would be to use a summing stage as the last stage; you might be able to lump that in with your amplification stage as well.