I got confused a bit on what you were saying above, but basically:
If you are building a 3 phase machine and are using 3 coils in series for each phase, then make one test coil with a known number of turns equal to a guess of what you think you will need, and measure the no-load voltages of that one coil.
To measure that voltage, stick the test coil in what will be the approximate final air gap between the two magnet rotors. Then spin up the rotor to a known rpm and record the voltage. The voltage obtained from the final coils will be proportionate to the number of turns in the coil, and proportionate to the number of rpm.
Because of this we then have all of the information we need to design our coils. For each phase the coils are connected in series and placed such that the magnetic flux across each coil is the same at any instant in time, the output voltage is the sum of the AC voltage from each coil (when doing your final assembly make sure you have them connected correctly so that the voltages add). Then the open circuit voltage of the wind turbine in AC can be calculated. If you connect the phases in STAR configuration this would be the voltage from one phase (3 coils in series) multiplied by the square root of 3. For Delta, the calculation of the final output would be just the voltage of one phase.
Thus if you know the rpm and voltage output of your test coil, you can figure out how many windings per coil are required to reach your desired cutin speed. The output of your alternator is AC, and then you rectify it through diodes to DC. if the battery voltage is around 12.6, you will actually start pushing a little current into them when the AC voltage is about 9.7 volts, as the peaks of your sine waves will be the square root of two times that voltage and then take off the 1.2 volts or so lost in rectification and you have your 12.6 volts. That being said, traditionally, the cut in speed is taken to be when the AC voltage reaches a higher value at 12.6 volts AC (for a 12V battery) from the alternator from most of the stuff I've read as the alternator doesn't generally push much current, or slow the rotor appreciably below about that voltage anyway.
Now you can calculate the number of wires required for each coil. You can select the largest guage of wire (or wires if connecting several in parallel) that you can fit in the space available for each coil between your rotors.
Once assembled, you can adjust the airgap a little bit to increase or decrease the rpm required to start charging you battery as well if you don't peg it to your target exactly. When the alternator starts to charge, depending upon the resistance in the line to your battery bank, the rotor will become resistant to increasing speed as the wind increases, which can lead to a condition where the prop spins up and then if the winds aren't sufficient stalls out, then the cycle repeats. Increasing the air gap, or the resistance in the leads to the battery bank can correct that problem should it arise.
I don't know if this answers your question, and I'm sure others will have more to add, and may be better at explaining the phenomenon, but I hope that this helps you some.
Rich Hagen