Bypass capacitors around DC-DC converters
Tha diodes are there to absorb over-voltage (resulting in reversed current flow) shoved back into this power supply from the motors, I'm thinking.  Any inductive load can "return energy back to the source" and those diodes are there to absorb such energy.  Think of the reverse polarity diodes across relay coils, same thing.

Those input and output filter caps cover an impressive set of orders of magnitude.  I wouldn't change them at all.  This is an atomic force microscope, yes?  That's an amazingly precise instrument.  Those different caps are there to soak up noise and avoid self-resonance at different frequencies.  

If your AFM works now, good enough!!  Look at some atoms!!!