Hi,
Thanks for the diagram, but it doesn't show your wiring and pinouts.
Your 42Vdc dc-dc converters how are they wired in.
With the complexity and stage at which you have your project I would have expected a concise and labelled circuit diagram.
Do you have 0.1uF capacitors, they will bypass noise better than the 470uF Electo caps you have.
Place 0.1uF at where the wires go into the motor and where you terminate the supply wires.
0.1uF on each of your powrr supply output terminals too.
Tom.. 