JW, Google 'Arduino', there are thousands of pages on the different uses of this brilliant little microcontroller, they are very cheap (usually less than $10 each). Their uses are only limited by your imagination.
I will be using the Arduino in PWM (Pulse Width Modulation) mode, by monitoring the speed of the main shaft, so how it works is that when the main shaft is spinning at say 23 rpm, then the eddy Current Brake coil will receive a very thin pulse (maybe just a few milliseconds long) that will start to keep the main shaft speed in check. When the revs are at say 24rpm then the pulse width will be applied for a little longer, and so on, when the speed is at say 28 - 30rpm then the pulse width will really be starting to grab the Eddy Current Brake. I am not sure at this stage whether I need to use AC or DC applied to the brake coils (I think there needs to be two coils opposing each other, but to be honest it is only an idea).
The Permanent Magnets provide multiple pulses dependent on how many magnets are on the rotor, this would be in the order of 6 or 8 pulses per revolution. If there is a strong gust of wind, then the Arduino will react accordingly within just a few microseconds, but the concept that I am after with this control method, will be designed to always allow the alternator to generate power. As the revs decrease, then the Eddy Current Brake receives narrower pulses until they completely turn off, and the alternator generates what it can based on what wind is available. Very simple really.
I hope this answers your question?