How to get code-snippet to only 'loop' once?

Right now, if I restart the machine it forgets where the motor is positioned last time.

I don't see that. What I see is that you read a value from EEPROM, but do nothing with it. You don't print it. You don't make the motor go to that position.

  lcd.setCursor(0, 0);

  lcd.print("Pulses:");
  if (PulseCount > -1) {
    lcd.print(" ");
  }

  if (PulseCount < 10 && PulseCount > -10) {
    lcd.print(" ");
  }

  if (PulseCount < 100 && PulseCount > -100) {
    lcd.print(" ");
  }

  lcd.print(PulseCount);

This belongs in a function that you call from loop(), not in loop().

Your code is just littered with useless curly braces. Get rid of them.