I know you're getting paid (atleast I hope you are) but, that air scoop is the car owners problem. You shouldn't have to be doing battle with anyone to rectify the issue.
The owner of the car should be suing the previous shop for derelict of duties.
I guess at this point, if you can't fix what has been done to it, let the car owner know he'll have to take a $1,000 loss on that scoop that's going to get ripped off the car when it see's it first 100mph run.