Thank you to all for the advice. I'm still fuming over this entire situation, but have realized there is little point in letting it keep me awake at night. Last night, I acknoweledged that when I was the the MR, I took audits personally as it was "my" system being assessed (yes, a no-no, but it's human nature). Now I'm taking personally because I'm assessing the state of what used to be "mine" and seeing it not in as good a shape as it used to be.
It's kind of like your car that you opt to give to your younger sister while you go and buy a newer, nicer one. You babied that older car, regularly maintained it. And now you see her driving it into the ground. It's not your car any more, but you can't help but feel sentimental about it.
It's not worth leaving the organization over, this situation. But I have every intention of ensuring that my hands are clean. It used to be my system. By the time of the audit, it will not have been mine for 8-10 months. My former boss has been in charge for 1.5 years. Time to cut the apron strings. He needs to have some accountability for the state of things.