Creating a mobile engine for my baby son

// initialize the stepper library on pins 8 through 11:
Stepper myStepper(stepsPerRevolution, dirA, dirB);

The code and the comment do not agree. Fix, or delete, the comment.

void setup() {
  // initialize the serial port:
  pinMode(pwmA, OUTPUT);
  digitalWrite(pwmA, HIGH);
  pinMode(pwmB, OUTPUT);
  digitalWrite(pwmB, HIGH);

  // Turn off the brakes
  pinMode(brakeA, OUTPUT);
  digitalWrite(brakeA, LOW);
  pinMode(brakeB, OUTPUT);
  digitalWrite(brakeB, LOW);

  // Log some shit
  Serial.begin(9600);
  pinMode(pin_A, INPUT);
  pinMode(pin_B, INPUT);
}

What shield are you using? 90% of what you are doing here is wrong.

Is the rotary encoder attached to the stepper motor? If not, a simple potentiometer would be a far better choice of hardware to select the delay() interval with.