How should I make a generator-powered rectifier/regulator charge a battery?
If you are using a 6volt battery then for most of the time you need a boost switching regulator except for those periods when the generator might be producing voltages at about 6volts. The problem here is that the generator is about the same voltage as the battery and this effectively means using a boost switching regulator generating maybe 8volts followed by a buck regulator that takes the 8volts and charges the battery thereon.

The alternative is to use a 12volt battery and avoid the buck regulator. In effect you just have a boost regulator and it will be about 90% efficient.

Ensuring the battery does not lose energy back into the charger when the generator is stopped is trivial so you have to decide on your battery voltage and your battery technology. This, might warrant a fresh question should you struggle to decide.