Knowing what kind of tune is on the car is crucial. For example, was it tuned for 91 fuel and somehow got a tank of 87? I once went home to visit my family in Missouri and no 93 available in my home town. I was stupid and put a few dollars of 91 in the car, just to get me to the next town. You guessed it. My motor with a tune for 93 did not like the 91 at all and by the end of the day I was $800 in the hole with a new set of injectors, new plugs, shop labor and diagnostic fees. The codes it was throwing were very similar to ones you've listed above. The only difference was that I was already running an off road x-pipe with no cats and I had a misfire on #7 cylinder instead of #8.
I can promise that none of these guys are making a dyno suggestion to be crappy to you, but Ford's pro cal tool is very specific in what it does. If so much as the air intake was changed then it will not account for it.
Step 1: Are you sure about the fuel? (Fiance didn't pump 87 while you went to take a pee?)
Step 2: Are all of your sensor connections and wire harnesses in good shape (nothing accidentally rubbed or burned through) and are they all plugged in?
Step 3: Are there any vacuum leaks in the intake or PCV system?
Step 4: Are one or both of your cats blown out? If you were running rich and had fuel build up in the cats then the exhaust can act like a blow torch, melt the cats and clog your exhaust causing all kinds of hell.
step 5: Do some research on line and in your area to find a shop that does Mustangs or a Ford Racing/ SVT dealership that has a tech who know his ass from applebutter when working around a supercharger.
Your description sounds rough. I've been there and it sucks. I definately feel for you. Be careful not to spend a thousand dollars replacing perfectly good parts before you consult a professional. It can happen before you know it. Haynes manual is a good tool, but it's written for people who already know their way around a car and it won't begin to touch a supercharger issue. FYI. A Haynes manual will help you change your brake pads, but will be pretty useless for this issue as you've described it.
Best of luck, seriously. Let us know how it turns out.