After lots of struggling with the current perf board electronics, we decided getting a PCB made was the way to go. The electronics have changed quite a bit since the last version so I started this one from scratch.
Changes include many more connections to the arduino, headers to connect the H-bridge and RTC breakouts, and removing the MOSFETs. The PCB includes a proper ground plane, our logo, and holes for mounting!
The primary benefit of moving to a PCB is the ability to use a rectangular connector on the board and insulation-displacement-connector for the ribbon cable, which means that we will be able to snap the 50-wire cable on and off the board. The quantity of connections made for a messy perf board and caused a lot of headaches while troubleshooting malfunctions. Despite the current setup working, it wouldn't be reliable in the field.
There are a few changes I need to make to the design, such as optimizing the sizes of the VCC traces, but it should be sent out to be manufactured soon!