Monroe had problems with the top nut of their quick struts a few years ago, being undertorqued. It's possible KYB has that problem, too. Otherwise, it's the mount.
Yes i called the Ford Dealership locally. Its a known issue with the OEM springs to break in these years lots of them in the Fusion forums etc. I asked if the part had been updated or changed they said no.. so i would be replacing a faulty part with another faulty part. I also had the throttle body failure like alot of the others and yes i bought the OEM part to replace it with knowing its going to have a short life as well.
KYB as far as i have read over the years on here have been a solid choice until now in my thread..they are dogs.
The clunking sound im hearing is dissussed on many google searches and alot of the fixes have been tightening that nut.. I wont know until the mechanic gives it a shot... but i just dont see the clunking being the struts bottoming out with the extra 2 inches of travel it now has.. and i dont see how both struts were shipped defective. Ive been wrong before though.
Some people have problems with KYB's aftermarket strut mounts. They seem to get the most complaints about their strut mounts compared to Monroe and other brands.
A lot of people who don't like quick struts complain about generic spring rates and poor quality mounts. Supposedly, almost all aftermarket OE replacement springs (Moog, etc) are made by the same factory.
You could also get H&R springs, though they do lower the car 2 inches. Steeda also makes springs for your Fusion. Another option is Racing Beat springs for the 03-08 Mazda6, which lower less than an inch
Those are likely the only aftermarket springs that are better than OE, except maybe OE Mazda springs from the Mazda6, but Mazda does have a bad reputation in terms of rust.
Any of those springs, OEM/Motorcraft strut mounts, and Bilstein shocks would be the best combo if you say no to quick struts.
Ford and Honda are the only ones to offer OE quick struts with OE springs and mounts from the dealer. Honda charges much more for theirs, while Motorcraft quick struts are more fairly priced. Mando offers some OE quick struts for some of the cars they are OE on, mostly Hyundai and Kia.