Yes, the port-to-pin assignment is messy. But, the PCB layout is much cleaner. All of this could have been avoided if Port G wasn't broken up all over the processor, but it is what it is. Could I have aligned the port with the display? Yes, if I hadn't been under the impression that the port-to-pin mapping was taken care of by the pins_arduino.h file for Megacore. I simply put the LCD pins in sequence with the "pin number" assignment.
Megacore pinout:
My PCB:
With this layout, the display is physically supported by the thicker uC PCB, and the uC PCB is mounted on standoffs to the front panel-keeping the display in place without resorting to double sided tape or the like.
The rest of the project is well underway-so far half of my digital IO is working, the panel buttons and rotary encoder are working, the analog inputs are working properly, and the serial console is responding correctly. The TWI interface and encoder code both work together, but not on this board yet (development of each section of code was done on an Uno over the last year) and the display code will run, the serial console responds correctly, the control lines are working, but the data bus is still scrambled, so no display yet.
This is the display I am using, Link To Banggood blue display