new turbo, probably not unless its damaged or defective
100k warranty, i would ask for the details in writing, since your in the post 36k miles warranty arena, it may be good till 100k as is the rest of the oil covered items, I would ask, it seems to be an area of unclear thinking, some folks get the warranty extended by ford and some dont for an additional mileage period,
as far as a 04 motor being replced by an 06 motor
you will more than likely get a reman engine which is just as good as new
or could even get a new crate engine. again ask the folks doing the work.
or they may just rebuild yours if the block is not ruined, to many variables
best thing is to ASK the service manager,
see now you have more questions than answers, I should work for the IRS