AC current sensing and fft

My project is to make differential protection with harmonic restraint for a 2 kva transformer so for that I have to sense primary and secondary current , I have designed cT which 1100:1 ratio , hence my 10amp current reduces to 9 ma and by providing potentiometer at output I can convert is into nearly 2 volts ...... So my question is-

How can I bias two analog input pins for both the current ......? And how can I perform fft for both inputs to segragate different frequency content