Storing MAC Address in EEPROM via Serial ASCII input.

First if the ascii representation for Hex A is written as a little "a" or as a caps "A", the conversion will be different.

Yes. But, it is easy enough to manage that.

char MACstring[] = "ab,cd,ef,AB,12,CD";
byte MACvalues[6];
byte index = 0;
byte val = 0;
byte num;

for(byte i=0; i<strlen(MACString); i++)
{
   char ltr = MACString[i];
   if(ltr >= 'a' && ltr <= 'f')
      num = ltr - 'a' + 10;
   else if(ltr >= 'A' && ltr <= 'F')
      num = ltr - 'A' + 10;
   else if((ltr >= '0' && ltr <= '9')
      num = ltr - '0';
   else if(ltr == ',')
   {
      val *= 16;
      val += num;
      MACvalues[index++] = val;
      val = 0;
   }
}

At the end of this loop, MACvalues should contain 0xab, 0xcd, 0xef, 0xAB, 0x12, and 0xCD. You can then store the 6 bytes in EEPROM for later retrieval.