Just to recap the functions of the original regulator (correct me if I'm wrong)
1) connect generator to battery when generator supplies more volate than the battery,
2) Regulate the output voltage (by controlling the field),
3) protect against overload.
I can easily use blocking diodes to curry out the function of "cutout". I can regulate the voltage by PWM the field coil. I'm not sure on current limitation yet though, I can easily cut the power by turning off the field coil but I'm uncertain of the method of detecting the overload and then what to do about it as I can just cut power (but for how long ?) or i can lower the voltage (reduce field duty cycle) until the current is under control and keep it there. I could then have a warning light to signal under voltage which should make anyone looking for fault understand that there is a short, at the end of the day if there is a short the battery will supply most of the power