It sucks that you lost out on the $900. But you may be able to reclaim it with a civil lawsuit and all legal expences to file the complaint, based on the fact that you authorized the repairs based on the shops diagnosis.
As a side note, if you are still having that "whine" sound coming from the rear of the vehicle, you may want to change out all the factory hose "spring Clamps" with some good quality "screw type" hose clamps..
My sister has an Expedition that had a whine sound coming from the rear of the vehicle and it turned out to be the whine was coming from a small vacuum leak in the fuel tank hose's. The hoses were good, but the factory "spring clamps" weren't sealing the hoses to the metal tubes of the fuel tank. And the vacuum created by the emissions system was causing the sound. It also set off her trucks "Check Engine Light" with the code that showed "small EVAP leak".