C4D capacitively coupled electrode sensing - circuit simplification
There's a method of measuring small capacitances and their variations that I find quite interesting and it's much simpler than the circuit you're working with. This method is used in capacitive touch sensors.

The method requires only a digital I/O pin from a microcontroller connected in your sensor device (which is the capacitor). It works by sending micro pulses of constant duration and reading the value back. Now, as we are talking about digital inputs there exist a voltage threshold where the microcontroller starts reading as logic "1". The amount of pulses that are necessary to charge the capacitor so it reaches this threshold and input value changes from "0" to "1" is directly related to its capacitance.