For SNR calculation, should I use FFT|X+iY| or FFT|R|?
To calculate the SNR you need to get the signal's power. One way to do this is in the time domain, but Parseval's theorem says that the power in the time domain is equal to the power in the frequency domain as it should be..it is the same signal after all. The DFT version of the theorem is $\sum_{n=1}^N|x[n]|^2=\frac{1}{N}\sum_{k=1}^N|X[k]|^2$, where $X[k]$ is the DFT of $x[n]$, which means that the power will be determined by its magnitude squared and the phase has no part in the calculation.