Sorry for my delayed response, I've moved on from this and have other stuff on my mind. I have also completely lost interest in the Due for a couple of reasons.
I have made all the above changes though and will post a new version soon.
Negative logic annotated.
I don't think I'll add those two LEDs as they are not really part of programming the Due for the normal application. I'm happy to be convinced otherwise though.
Hardware pins are now black on light blue, GND still the same. As that's the only use for that combo even if the text blocks out and it just prints black it's obvious what it is I think.
I've added the Arduino pin #s for those three SPI pins, it's a bit of a kludge because there was no room but doesn't look too bad.
I think you are right about that, D70 and D71 were correct but the other labels were reversed.
@anyone with a colour printer
Let me know if the current colour scheme works, I don't have a printer so can't test. Bear in mind though that all printers are different, if it doesn't look good on a $20 Inkjet I'm not likely to change anything unless a few people have trouble.