As someone who DOES abuse the car and driveline, I can tell you... No way you did ANYTHING that could cause this clutch to fail under stock or even a couple bolt ons with a stock tune. If your clutch fails with 18k miles its because it was bad, or your 17 years old and just wore it out. Of course... If you wore it out, they would have seen that a few days ago, so its not worn out.
I'm telling you, NO AMOUNT OF ABUSE will cause this clutch to fail unless its build to a lesser standard than mine. I'm flat-foot shifting with bigger tires and 354ft. Lbs of torque at the wheels and the clutch is not failing or slipping. Even when the bigger turbo was installed making 250whp+ at redline and flat foot shifting, my 25-26k mile clutch has been flawless ( knock on my wood ).
That call to them letting them know the clutch was making noise should make ANYONE with reasonable logic understand it was an issue with the install. If the clutch was bad during engine replacement, they should have said something.
I'm a fairly well paid tech myself. We are NOT held accountable the way a ford tech or dealership tech would be, but my techs STILL try to slip out of any ownership of wrong doing. They refuse to own up to mistakes. They consistently side step responsibility or try to pass on fault to the operator, part supplier, or another tech. And these are well paided tech's WITHOUT a paying customer ( its a fairly large cooperation ). So the idea of a tech trying to deny fault or wrong doing is nothing new to me. The real issue is the dealership NOT STEPPING UP. As the employer, they assume responsibility for this tech and thing he may drop the ball on. They should do two things. Protect THEIR NAME, and FORD by getting all hands on deck and have senior techs (with the tech that screwed up ) get this car back on the road ASAP. The second thing they need to do is have someone figure out WHAT WENT WRONG, and have a class or meeting about what they found, how it happened, and how to make sure it never happens again. This adds value to every tech they have, provides customer service, and everyone is better for it at the cost of WHAT? $450 in ford parts cost and $300 in dealership labor, and you'd have pretty much a guarantee than no fiesta ST or fusion 1.6L manual trans would be scewed up again at your dealership. That's cheap education to me... But then again... I'm one of the rare techs that own my mistakes, point them out to others, and share my screw ups so that others may not suffer the same issue.
On the other hand.... When you pay guys peanuts to work on complex cars/trucks. You get what you pay for. There is a reason I don't work for Ford or any other dealership.
I would not accept anything else but them fixing the damn car COMPLETELY, on anyones dime but yours, WITH A RENTAL. The rental and the clutch being on back-order is likely the biggest issue.
Its un-real to me that your engine died, and now they are passing issues caused that repair onto you. I'm pissed off that someone else is doing that to someone else... No one is perfect, but at least own your mistakes, that's what being a man is.