Stepper motors (apart from very low power ones) should be driven by a constant current chopping controller, which is not what you are using. If the stepper motor is getting to hot, you need to either reduce the voltage it is getting (e.g. by using a lower supply voltage, or putting a resistor in series with each winding), or use a constant current stepper motor driver instead.
What size is the stepper motor, and what is the resistance of each winding? Those figures should give us a clue about what current it needs.
What size is the stepper motor, and what is the resistance of each winding? Those figures should give us a clue about what current it needs.