How to choose a cut-off frequency by interpreting FFT
When you are doing an FFT over a large signal sample you obtain the peaks at the frequencies that the FFT encountered over that sample. However, the amplitude that you see for each peak is proportional to the 'time' that specific frequency component existed during the whole signal sample.

Imagine for example you have two acquisitions: one with a 1-second vibration at 10 Hz, and another with same 10 Hz vibration occurring for 30 seconds. 
The amplitude of the 10 Hz peak for the first acquisition is expected to be 30 times less than for the second acquisition. 

I expect that the largest component you have is DC, which has a much higher amplitude than the other frequency components you may have.
One quick hack is to remove the DC component from your signal, before doing the FFT.
Calculate the mean of x and then x = x-mean.

You may also use a spectrogram, which calculates the FFT for smaller windows. This will give you a 2D plot with the time in one axis and frequency in the other, and the color corresponds to the amplitude.