I'm Mechatronics Engineer with experience in robotics, servo-mechanism, virtual reality and cyberphysical systems.
There is a php I/O extension to handle the serial port.
Also you need to be careful by making a division between the power electronic, and the control electronic; to avoid damage the serial port. (H-bridge, optocouplers, diodes, etc)
Besides you need to solve what kind of stepper motor is better. (Voltage, current, torque, advance degrees, etc).