1. Yes, for example, pin 2 might be used as an 'output' for the step or direction line to the BOB and subsequently to a driver
2. Yes, for example a probe input
3. Generally, you will use a 'pull up' or 'pull down' resistor on the input pin. if it is a pull up, the input will read 5V and when shorted to ground, 0V
4. Many people have tried and to the best of my knowledge, none have succeeded.