Op-Amp with Voltage Controlled Gain and Unity DC Gain
One issue is that the filters to get rid of the PWM may be attenuating the signal you want to measure, so I would suggest a notch filter to get rid of much of the PWM signal.

The Fliege notch filter is a versatile and somewhat forgiving filter, and I have run one up for the 20kHz:



It has this simulated response:



The notch depth is -55dB here, although I would expect -40dB as a more realistic response with real devices and layout. The bandwidth between the -3dB points is about 2kHz. 

As this filter is unity gain at DC, it would be simple to introduce a DC offset to run on single supply.

Note that R7 is only present to enable the simulation to converge, and the notch depth is proportional to the ratio \$ \frac {C_0} {R_0} \$

You could then use a high pass filter to attenuate any harmonics of the PWM drive signal which may simplify the rest of the signal chain.