IR and Photodarlington circuit doubt

concept:
I use IRL81[LED] as source of 1KHZ 50% duty cycle PWM and OP560A[photodarlington] as Photo detector .
Connecting source and detector via Fiberoptic with small Portion decladded where different samples to be introduced.
When samples introduces in the decladed fiber there is a Changes in intensity. This change in intensity changes the Photo Darlington(PD) voltage
now i need to find the difference between the reference signal 1khz 50% duty cycle PWM and PD.

prob:
Need to detect change in amplitude as well as phase.

i recently posted same question here , i'm getting confuse with the followup's

Working model: i used 1khz 50% duty cycle(don't get confused as shown in Image 100hz)

 

http://forum.allaboutcircuits.com/attachments/20151010_134021_800x580-jpg.92766/
http://forum.allaboutcircuits.com/attachments/capture-jpg.92776/

you can see image here.

yes the change in IR level is very small and the output of the PD is in Millivolt