In your diagram #46, you still do not show everything - the -ve wire of your top 12v supply, needs to be earthed to your Arduino earth. Also, you do not show what powers the Arduino!
I think it is best to start all over (new Mega) - use LED's via a 1K resistors, instead of those driver boards. Just see if all works then, then add the driver boards again - see at what stage the smoke comes back - if ever.
I know its work, but, we all want to see this circuit working for you!