If you are using a shielded loop then the Loop Antenna Amplifier head unit PCB can be mounted in a shielded metal enclosure. The head unit has two separate grounds separated by a common mode filter. Without running some tests I'm not sure which ground to connect to the metal enclosure so try running a wire from the box to either ground plane on the board to find which one is most effective at reducing noise with your shielded loop. I suspect that the enclosure to the ground plane on the loop rather than the coax input will give best results.
The base unit can also be mounted in a metal enclosure. Connect a wire from the ground on the board (USB shield) to the metal box. You can also connect the metal enclosure on the base unit to ground to reduce noise and conduct any static electricity on the antenna to ground.
A shielded loop will work well at 60 kHz. The problems with them occur at higher HF frequencies where the loop inductance and capacitance to the shield form a resonant circuit.