Averaging multiple FFTs in matlab
Welch’s method is a scheme to reduce the fluctuations (noise) in spectral power estimations when you have only a single time sequence with which to work. Because you have multiple time sequences, I’m not convinced that Welch’s method is what you want. If you have time sequences $x1(n)$, $x2(n)$, and $x3(n)$ of different lengths, I suggest you zero-pad the shorter sequences so they’re equal in length to the longest of the original $x1(n)$, $x2(n)$, and $x3(n)$ sequences. (It’s my guess that no time-domain Hanning or Hamming windowing is necessary.) Perform three FFTs and compute the three corresponding spectral power sequences $P1(m)$, $P2(m)$, and $P3(m)$. Finally, average the three spectral power sequences, element-by-element, as:

Spec_Pwr_Ave = P1 + P2 + P3;

Then plot your ‘Spec_Pwr_Ave’ power-spectral sequence.