Is this circuit block diagram correct?
I wouldn't bother with a buck converter to charge the capacitor.  Just connect the output of the full wave bridges directly to the capacitor and use a shunt regulator to make sure the voltage doesn't go above whatever level you want.  Just a zener diode might do.

You don't really care what the load on the motor is when the capacitor is already full.  Besides, stepper motors are pretty crappy generators, so you probably won't notice much of a load change on the shaft anyway.

Also, are you sure your boost converter can run from only 600 mV in?  That's quite low.  A bootstrap supply might help.  This means the boost converter needs a higher voltage to get going, but once it does, it makes its own power supply voltage so that it can work to a very low input voltage.  Basically the boost converter electronics get power from the same voltage the LED is being run at, with only the input power coming from the capacitor.  There will also be a Shottky diode from the cap to the LED so that when the cap is at 2.5 V, the boost converter has 2 V or more to operate on.  You can definitely make a boost converter that runs from that initially, and then over 3 V once it starts up and runs the LED.