You're trying to cover too much territory at one time. Your idea of using the shorted second alternator to hold the turbine speed fixed won't work because nature won't cooperate. As the wind blows harder the mill will speed up. At 50 mph the wind has 8 times as much power as at 25 mph, and that power will act to make the blades spin faster. One result will be to cause more current to flow in the coils of the shorted alternator, eventually causing the alternator to burn out. Simple wind resistance of the mill will also increase, possibly causing the blades to break or hit the tower. Furling the mill tends to alleviate these issues within limits.
You are also confused as to how the voltage is induced in the coils. If a coil is smaller than the diameter or area of the magnet face so that it sees a constant value of magnetic flux as it moves relative to the magnet (nature doesn't care which is actually moving), no voltage will be induced in the coil. A voltage is induced when the magnetic flux changes, such as when the coil passes from over a north pole (region of positive flowing flux) to being over a south pole (region of negative flowing flux). In a properly designed 3 phase alternator the maximum voltage will occur when the coil exactly straddles two neighboring magnets. conversely, the voltage will be momentarily zero when the coil is exactly centered over a magnet.
The voltage induced depends on the RPM of the alternator and the number of magnets. For instance, with 12 magnets the rotor will have to advance 30 degrees for a coil to pass from centered on one magnet to the next, which generates a voltage pulse. For a given RPM the time it takes will be the same no matter how the coils and magnets are arranged, so the induced voltage should be about the same even though the size of the rotor would be different if say 2 inch by 1 magnets and associated coils are turned 90 degrees. You should go read up on Faraday's Law.
