Creating a 1KHz clock O/P

If the circuit does what you want it to do there's no need to add superfluous GPIOs.

As the basis for a prototype, I don't see any immediate problems with the circuit. Given the intent to use it in a hostile automotive (motorcycle counts...) I assume you'll do a lot of testing and qualification (e.g. tolerance to electrical and RF interference, operation at temperature extremes, vibration etc) before committing to use (personal) or sale (commercial.)