So after my integration testing ( You WILL be integrated! ), I realized that the routing of the cables and signals between the boards wasn't very optimal. I had already come to conclusion that I needed new PCBs to fix a bunch of small design issues, so I decided to overhaul the connections. I spent an entire evening making some mockups and routing cables to figure out the best way to connect everything, then updated all the design files, and ordered new PCBs. They should be in later next week! Fun Fun Fun!