I assume the decoupling beads
Beads? They do nothing, only fit for putting round you neck.
You need ceramic capacitors for high frequency and large electrolytic for lower frequencies. The whole power to the motors would also benefit from a seriese inductor, like I said before.
After a bit further research it suggests I have built a guitar which is amplifying the stepper frequencies.
Does that mean your casing has resonate frequencies that are excited by the steps in the motors? If so a micro stepping driver will help reduce these.