I passed emmisions with flying colours too on failing Cats. I was new to the car and there was a leak in the EGR as I recall
so right there not all the exhaust was making it out the tail pipe. Anyway. Point is. Clogged cats may not have much effect on emmisions as less gasses will make it to the sniffer. I'll bet in your case there is a tonnes of performance loss by this point and you may not even notice it. What you say about the reflash though is very interesting too. Sounds like something Ford would or could do.
