So, after a two day break fiddling with coils and fets I have it working. It's still a little 'rough' around the edges, and I faked the windmill coils with a small transformer.
Thanks to Victor for an excellent idea.
The principle is very simple, and it turns out the practice is too, the coils in the alternator have enough inductance to 'reuse' them as boost coils in a boost convertor as seen in this schematic.
So all you really need is a way to short out those coils...
The trick is to have one fet per phase, each fet handles a 'leg' from the coils. The fets then replaces the lower half of the diodes in the full waves bridge.
The gate gets driven with a very low duty cycle (about 3%) signal of 5 Khz.
These spikes will push all the fets into conductance at the same time, effectively shorting out the coils (mosfets have very low 'on' resistance). Upon the release of the gate voltage at the end of the pulse the current in the coils will induce a huge voltage in the other direction, and this is enough to overflow into the batteries. The effect is the same as a 'regular' boost converter, you save yourself the cost of the coil, and you're switching the AC side rather than the DC side, which makes everything very elegant.
The practical upshot of this is that you can start charging at ridiculously low wind speeds.
One issue with more powerful windmills is that the parasitic diode in the fets is used as the rectifier, which will work but on a more powerful windmill will probably fry the fet sooner or later (likely sooner). To remedy this you'll have to place a schottky diode parallel to the fet, the schottky diode has a forward voltage low enough to relieve the fet from the current.
The cost of the circuit is somewere around $5 in parts, one 555 a bunch of fets and some cheap passive components. You could feed the 555 from an extra set of diodes on the coils, a cap and a small supply, to make the circuit non-parasitic.
Tomorrow I'll draw up a schematic and give a proper explanation of this, right now I'm just happy.