Use the right tools for the job! While I love Perl, you may want to consider using tools designed for this particular subject. The biggest problem with Matlab is the cost, but there are alternatives - http://www.octave.org/ for one!

On the other hand, if you know the math (I had a great book, but I can't find it now) and you want to take on this challenge go for it. If anything you will learn much more about FFT, then you do now. There are many more applications for FFT then you probably realize.

Just my 2 cents.