welcoke aboard rattlesman!
i have no direct experience with those exact machines, but i do have an idea of what's going on. the thinner/higher turn phase is there to give the turbine an earlier cut-in for a small trickle of power in lower winds, then once the machine starts really moving the other two thicker/less turns phases hit their cut-in to really push the amps. the largest thing i'd be worried about, would be the thinner windings burning up if the furling/speed control is not dialed in correctly.
yes, you can run three wires down the tower and rectify at the base with three full wave bridges, then run your single phase to your battery bank. (assuming these aren't grid tied). it seems many small commercial turbines don't use large enough rectifiers and/or heat sinks. so find some big pieces of aluminum to mount your new rectifiers to!
adam