That's not what I meant, but if that's the way to do it...
My thoughts:
Register - Prompt for payment (the way it is now)
A. If they pay, then Email confirms registration and payment B. If they don't pay, then Email thanks for registration and includes payment link and check instructions
Follow-up for non-payers is not a bad idea, but daily reminders for someone who already mailed a check is going to annoy. Optimally it might be an Email a week before the Event or something like that.