Q. - The pin definitions on this page look very wrong to me, there are about 5 pins with numbers above 53 (mega has only 53 DIO)- do these refer to DIO via the analog port?
A. - You are correct. You can use the analog Arduino pins as digital by calling them pin numbers higher than the highest digital pin number on the board. So to use Analog pin 0 on Arduino MEGA as a digital pin, call it pin 54, Analog 1 = Digital 55, etc.
Q. - It also bears little to no correlation to the pins.h in sprinter master
A. - There is a pull request submitted on github to add RAMPS 1.3 to Sprinter's pins.h. In the mean time, it is in this fork https://github.com/johnnyr/Sprinter/blob/master/Tonokip_Firmware/pins.h
Q. - Step 10 under Shield Assembly is wrong. The caps should be C5, C8 and C1 and the positive leg is down the bottom (negative line at the top).
Q. - Is there a mistake with pin48 on AUX-2 in Arduinomega1-3connectors.png? On my RAMPS 1.3, the pin is in fact D40.