RFID module software serial + serial read

  mySerial.listen();
  Serial.println("Serial number will be displayed here if a card is detected by the module:\n"); 
  // set the data rate for the SoftwareSerial port 
  mySerial.begin(9600);

You
You can't listen() to an instance of SoftwareSerial until AFTER you call begin()!

    int c = mySerial.write( CMD[i]*16 + CMD[i+1]);

Have you looked at the documentation for the write() method? Does it really matter how many characters you are writing? Why are you ADDING two characters? That makes NO sense.