Hi,
I know nothing about the such a use-case, so I could be totally wrong, but perhaps it could be worth examining to rule in/out TI's FDC range (e.g. FDC2214), they can operate in a differential mode, and can sense tiny changes with 28 bit resolution, and very low noise, and supports measurements up to 4 ksps, although that rate is if only one channel is measured. There are low-cost evaluation boards for the FDC series.
I played with one for a bit, you can do neat things with it such as create dust sensors and so on, detected by the minute change in capacitance.
Technically it doesn't measure the capacitance directly, instead, it measures the frequency of oscillation of a tank circuit (LC circuit), to 28-bit granularity.