Stepper motor power supply causing large ripple
There is no need to over complicate your supply, and putting inductors in will seriously cause problems where the current drawn (by the stepper motors is  pulse in nature). 

You simply need to increase your filter capacitor and ensure your diodes have a peak current capability at least twice your load current (so about 12A rating).

To calculate your filter capacitor size is simply:

C(F)= (I(Load) * (1/2F)) / V(ripplemax)     //2F because you have a full wave bridge rectifier

 (6A * 8.3 mS) / 3V  --&gt; 16000 uF


I selected 3 V ripple here, but you can select whatever you want. 

The output peak DC voltage is about (1.4 * Vrms) - (2 * diode Vf)

The minimum is V(outputpeak) - V(ripple)