To clarify a couple of things, such as the PCB arrangement, how the Pi and the Arduino communicate, where timing is done, below are a couple of schematics.

Overall schematics: How the Pi, camera, Arduino and PCB are connected to each other and what each part is doing.

PCB schematic, how components are distributed on the PCB according to location and functional module

Python software schematic: How the different independent classes relate to each other