In circuit tester (Pass or Fail Conflict)

  if (digitalRead(pinArray) == LOW && !ShortedOnPcb(a,b)){       // Has the pin been pulled low by a short?
    Serial.println(" ****FAIL****");
  }
  else 
{
    Serial.println("PASS");
  }

Then add the ShortedOnPcb() method:

boolean ShortedOnPcb(byte outputPin, byte inputPin)
 {
  switch(outputPin)
 {
    case 2:
      return (inputPin==10);
      break;
    case 23:
      return (inputPin==44);
      break;
  }
  return false;

I can't follow your code without the declarations. Put those in there explaining what outputpin & inputpin mean. I don't know what the reason for this naming is.

the only problem i have is that some of the pins are shorted through tracks on the PCB board i wish to test, What i now need to introduce into the code is a way of saying the 8 pairs of pins that are shorted are still passes even though they are returning a high reading.

For example
Pins 2-66 are all tested against one another they are taken for a one dimensional array one at a time and tested.
All Pins except (2 and 10) (23 and 44) (24 and 30 ) (29 and 31) (32 and 33) (39 and 41) (42 and 47) and (55 and 60) will return a low and a pass but the above pairs will return a high and a fail,
What i want my code is to acknowledge these high as passes.

What I mean is, like with this,

boolean ShortedOnPcb(byte outputPin, byte inputPin)

(2 and 10 )
(23 and 44)
(24 and 30 )
(29 and 31)
(32 and 33)
(39 and 41)
(42 and 47)
(55 and 60)

Can you tell me which of these are Inputpins and which are outputpins ?