The shop will charge you for the clutch, that's almost a guarantee. Has nothing to do with any extra labor, more to do with liability and their own insurance. Now the charge may be minimal, my guy charged me $100, but that included new cable and firewall adjuster installed with the new clutch and flywheel, that was with my motor out of the car. It does suck but sometimes it's the cost of business.
96 GT turbocharged - SOLD
97 Cobra vert stock -SOLD