Use of very large bulk capacitor for microcontroller power stability
You want to attempt to create a star ground where the power supply ground connection is in between the power and digital sides of the circuit.  Ground bounce is caused by resistive losses when a large current flows through the ground traces.  By putting the power circuitry on the "other" side of a star ground, you put the resistor that is causing the drop/bounce in series with the power load and not in series with the digital load.

Given your construction this might or might not be practical.