Robust Mechanical Design: A robust mechanical design will significantly simplify software and electrical requirements. Don't neglect mechanical design! Our mechanical design removed the need for 2-3 sensors and minimized drivetrain tuning.
Unit Testing (Hardware AND Software): Rigorously debug all subsystems (eg sensors, signal conditioning, communications, hardware-independent state machines, etc) before integrating. Premature integration leads to impossible-to-find bugs and eventually requires taking stuff apart to debug individually anyways.
Use the Scope: The oscilloscope is your best friend. At any point in development, use the scope to verify hardware and circuitry is working as expected, and then you can safely debug software.
Importance of Cross-PIC Communication Interface: Communication between PICs should be the first piece of software to develop! Well-designed communication can completely abstract away the multi-PIC setup in hardware, and greatly ease the software development process.
Plan Pin Layout: Take the time beforehand to map out pinouts, IC/OC/hardware timer allocations, etc. This is especially crucial if you can reduce your board count from three PICs to two by consolidating.
Plan Board Layout: Planning out where various PCBs/sensors will go will simplify wiring and minimize noise. Highly recommend isolating PIC lines on the power distribution board and completely isolating the Universal Signal Conditioning boards away from everything else where possible.
Start Soldering Early: Start transferring circuitry to PCBs as soon as possible! This will simplify electrical wiring and debugging. Also, the transfer from breadboards to PCBs will always have mistakes, and better to find those earlier than later.
Test Early and Often: It's impossible account for every case in software development, and you will find many bugs by purposefully testing for edge cases in adversarial scenarios.
Use Stranded Wires: Solid wires are supremely unreliable for crimped molex connectors, so don't use solid wires if you can help it.