Joe, thanks for posting my thread. I knew I had done something like this, but had stopped because it was a lot of work to lay out clearly in flow diagrams.
A lot of problems originate from plugging things in wrong. You know that the same style of connector is used for Analog inputs, Digital inputs, Digital outputs, PWM outputs, and Relay outputs. It's not keyed, and it doesn't come labeled.
I highly reccomend getting a adhesive-tape labeler and labeling each data cable on both ends. Also, mark up your motor controllers, sensors, Digital Sidecar, and Analog Breakout so it's obvious which way to plug the cable in. (It's not fun when you fry a $60 gyro because the cable was in backwards and 5v and 0v were reversed)
Here's an example of a marked-up Jaguar:
