How to filter noise out from large PWM system
I'd suggest you have a couple of problems with your design, particularly since you've mixed high and low current circuits on the same PCB.
You can add capacitive and inductive filters to your hearts content but you'll be chasing your tail for quite some time.    


Quite high levels of noise on the ground are acceptable if you have extreme isolation (PSRR) on the MCU supply lines. In your case you've used an LM7805 to supply the '328 VCC and this is inadvisable in a noisy environment.  Consider using a shunt regulator such as the TL431 from the 12 V supply to increase the impedance to that supply.
The TL431 is good to about 100 mA so should be enough for your '328. 
Your serial connection between processors is another potentially noisy connection. It's usually advisable when connecting multiple MCU board in an environment like this to optically isolate these lines.
I'd assume you are feeding the same serial data connection to all boards (a single serial line from your source PC/MCU), so you could arrange the inputs to be multiple opto diode inputs in series driven by a single output from your source.