I was able to fix most of the issues with my Cougar this past weekend. I pulled my rear header and the lower flange was cracked almost all the way around. It was hanging on by a tiny thread. I had it welded up and had the shop weld in a flex section to my y pipe to prevent it from happening again. The stock 2 bolt setup is crap. I'd guess Ford wanted to save cash so instead of using a flex they use some cheapo springs to function as a flex which isn't compatible with aftermarket y pipes.
While I was swapping the header I found the source of my idle issue. My PCV line was resting on my EGR tube and had melted slightly to create a air leak. Oddly enough it was resting on the insulation jacket which should have prevented it.
After the header weld, new flex, and some new PCV tubing the car drives prefect. Woohoo! Just in time for the morning blizzard!