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I was looking at it and it seems to me that if I change the MISO, SCK, SS and MOSI to PJ7, PD4, PE7 and PE6 respectively in the firmware, I could wire the LCD to board much more easily all through EXT2.

Okay, it would actually require changing a fair amount of pin definitions, but most of the pins being changed are the ones not in use by anything else since they are unstandard to begin with. The cable would become much more simple. All you'd need is a 20 position IDC connector, the ribbon cables that come with the LCD and a sharp blade to make the adaptor.

I've included a picture to help with the outline, but the basic idea is EXTB with the unused 9-10 wires removed is connected to the end of the IDC connector. Directly adjacent to it and flipped is the wire coming out of EXT A with the last wire in the series skipping 1 pin to connect VCC to VCC.
I guess the question is, would changing the MISO,SCK,SS and MOSI pins be as simply as modifying their definitions in pin.h? Or would other issues arise? I understand that timing is important, would this just completely muck it up?

As I understand it, and I'm bot an arduino expert, you can't do that.
The MISO SCK SS and MOSI pins are connections to the hardware SPI interface on the arduino, other pins won't have the same functionality, so you can't just remap them.

I see. I guess I got confused because the SPI pins double as regular digital I/O pins (which I'm finding out basically all pins can do) and thought that that was all they were and were just favored by the firmware.

This idea actually spun out of my original idea where the B1,B2,B4,B6 wires bypass the pins altogether by looping into the upper portion of the IDC and continuing out the other side where they reconnect with B3 and B5. B3 and B5 aren't used, its just nice to have the wires run together as a ribbon cable till just before they reach the SPI connector. At the SPI end its just a matter of routing 4 wires where they need to go.

That basically means either than the VCC wire, you connect 2 ribbon cables to a IDC and route/solder or crimp 4 wires VS route/solder or crimp 18 as outlined in the RAMBo LCD wiki.