Pin 13 has the on board LED tied to it. Some digital pins have additional uses that allow them to work together to drive specific hardware but you can still use them (and pin 13) as an ordinary digital input/output. Also any of the analog pins can be used as digital I/o pins provided they are correctly initialized in accordance with the documentation. This means you may have more pins than you Think! I would try and use separate pins for the stepper parameters just in case you change your mind down the track. If you tie the pins together, be mindful the you don't exceed the maximum current that can be supplied. You could also consider tieing the pins straight to the arduino 5 volt rail to avoid using up any pins at all in your case.