What is the right way to extract particular frequency phase information from FFT? Signals acquisition:

Two proximity sensors are positioned Orthogonal to each other. These would be measuring the vibrations of a rotating shaft. 

Problem:

Each of these 2 signals has two dominant frequency components (2441 Hz &amp; 762.9 Hz ) in it. I don't know the phase and amplitude information. I'm interested in finding the phase of the signal at 2441 Hz and 762.9 Hz. I did the following process to achieve amplitudes and phases in MATLAB


Applying FFT to the raw signal and calculating Amplitude and Phase.

%fft for X signal
fftx=fft(X,NFFT);
% absolute value of the signal 
Xn = abs(fftx);
A = mean(Xn);  % I took the mean to get single value.
phase = unwrap(angle(fftx));
phase_mean = mean(alpha);

Filtering raw signal to specific frequency prior to applying FFT using Butterworth filter. ( In this example I filtered to 2441 Hz)

[b,a] = butter(2, [ 2440/(fs/2),2441/(fs/2)],'bandpass');
X_filtered = filter(b,a,X);
% Applying FFT to filtered signal
fft_filtered = fft( X_filtered,NFFT);
Xn_filtered = abs(fft_filtered);
A_filtered = mean(Xn_filtered);
phase_filtered = unwrap(angle(fft_filtered));
phase_filtered_mean = mean(phase_filtered); 

I did the same process as point 2 to filter to another frequency say 762.9 Hz.
My sampling frequency and other things are defined as follows.

L = length(X); % 50050 is length of signal
NFFT = 2^nextpow2(length(X)); % Zero padding to nearest N power 2
%Define frequency axis
fs = 1e7; % Sampling frequency
df = fs/NFFT; % frequency resolution
dt = 1/df; % time resolution
X_detrend = detrend(X,0); % Removing DC Offset


I've been reading a lot of other posts on the FFT phase and Amplitude.But I'm confused with most of them. In my case, I need to extract frequency particular information (amplitude and phase) to do further  calculation. I'm still unsure if using the filters is right way? Will FFT and filters alter the signal information in any way? Could someone enlighten in understanding the efficient way to extract amplitude and phase information from a signal of particular frequency component.
To estimate spectral component phase angle relative to shaft angle using an FFT of length N, first gather a sequence of N samples such that the shaft angle is known with accuracy at sample number N/2, then window with a Nuttal window and do an FFT shift before the FFT.  The  atan2() of the FFT bin result closest to the desired spectral component will produce an estimate of the phase relative to the center of the original sample window.  Adjust that phase by the known shaft angle at that N/2 sample point to get a spectral phase relative to shaft angle.

If you know the spectral frequency or use a frequency peak estimator, then the phase can also be interpolated between bins for increases phase estimation accuracy.  Interpolate phase by using a Sinc interpolation seperately on the real (even) and imaginary (odd) FFT result components before taking the arctangent.