There is a single ground in this design, but we did use ferrite beads to absorb any high-frequency noise coming to the connectors. Please see the two relevant sections below. Note that we ended up using transistors with a lower gate threshold for the level shifters, BSS138 instead of 2N7002 in the schematics.
Here is the mini-USB connector. The metal shroud connects to BOX which goes to GND via a ferrite plus a TVS,
and here are the level shifters. Note that BOX connects to two mounting tabs on the sides of the connector which are not pins. The black wire of the micro-serial cable (pin 2) goes to GND via a ferrite.
The CPU is direct connect to GND.