Question related to Deconvolution and Fourier Transform
There could be 2 reasons why your 2 time series have different lengths : 

1. They have a different sample rate

The situation

The sample rate of your signal is the frequency at which samples have been converted from the analog domain to the digital domain.
If 2 signals of the same duration have been sampled at different rates, the resulting time series will have different length( the longer being the one for the fastest sample rate).



The solution

The only solution to that problem is to resample one of your signals. For this, you will need an interpolation filter. In Matlab, the whole process is very simple. However, if you need to implement that in low-level code it's going to be more complex (lots of things to take in account). I won't go into technical details here, there's a lot you can find here and on the rest of the internet.



2. They have different durations

The situation

It's very much possible that your output signal has been recorded for a longer time than the input signal. In that case, you end up with 2 signals sampled at the same rate but with different lengths.



The solution

If that's the case, you're quite lucky as the solution is trivial. You just have to do something "zero-padding" which consists simply in adding as many zeroes at the end of the shortest signal as needed for it to have the same size at the other.



Additional info

There is however something that you have to consider with deconvolution : if your system has an infinite impulse response (IIR), your deconvolution will only give you an approached image of your transfer function. Think of it as for any function : if you only see part of the plot, the best you can do is to do educated guesses on the function's expression.

Moreover, depending on your sampling frequency and recording device, you might have a phenomenon of aliasing on your recorded response, and you will not see the frequency components that are above Nyquist's frequency.