Interesting. I've a friend in Australia who's been doing some work analysing rainfall using arrays of wire across long distances (details somewhere here: http://wiredlab.org/), and during a recent conversation he pointed me at this paper: http://www.icita.org/icita2004/abstracts/128-5.htm which seems to use another method (involving Primes) for calculating Fourier Transforms, and claims a 95% speed up.

Sadly I haven't had a chance to look into it in any great detail yet, although it's "in the queue" of things to poke at. I thought it worth pointing out in case anyone else might find it useful.