help to calculate phase shift in certain frequency(identified from FFT)
Phase shift in time domain translates to frequency shift in the Fourier transform. 

$FT of exp(j2πf0t)x(t) = X(f−f0).$

If there is a phase shift in time, the Fourier transform that you take is already shifted in frequency. Find the shift in frequency f0 and you should get the phase change.