At first I used an arduino to feed a pwm signal to a stepper motor controller and to take the input from the control box, but that seemed like a huge waste (overkill I mean). So I looked into other ways of generating a pwm signal and found 555 timers could do it. I had been meaning to learn about 555s and this was the perfect opportunity. Thanks to [amandaghassaei] via instructables, I set up this simple circuit:

which is a LM555 setup in astable mode.  With C=0.1uF, R1=3.3KOhm, and R2 = 68kOhm, it will produce a 50%(ish) duty cycle at 100(ish) Hz (which I found to give a good speed).

Here it is integrated into the rest of the circuit

I setup up a DPDT momentary rocker switch to power the LM555 thus initiating the PWM signal to the stepper controller, but also to pull the DIR pin low when toggled to one side only. The DIR pin then got a pullup resistor to 5v. This enabled the switch to control the direction of turn without the micro-controller.