The short answer is that the payment system I was using at the time had no easy way to do this programmatically. Remember, a chargeback is not a missed payment. I would receive the payment on time, and then some arbitrary 15-20 days later I would get a paper envelope in the mail notifying of a chargeback with last four credit card numbers XXXX. It was a mess.
But yeah, all these are good points and also reasons I shut down the business. This time around I can apply all these lessons learned.