Very sad to hear this kind of thing
Did you sign an estimate or anything when you dropped the car off? If so did it have any disclaimers? If you didn't sign anything that has lots of protection for the shop than you may be in a better position and certainly you will have a fight on your hands to get them to pay for repairing the burned wiring harness. Its hard to imagine how they burned the harness because most of the wiring is fused. But it is possible to do that from a clumsy act. I would get witnesses together that knew the car wasn't burned at least was better off before dropping it off then go to small claims with them (written claims are not admissible)
You will not have much luck trying to get the cost of the parts down much if at all but the damage they did should be fixed at their expense and not by them, obviously they are incompetent to the degree they would even botch the repairs up or keep it another couple of months!

good luck!

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'95 E320 Wagon my favorite road car. '99 E300D wolf in sheeps body, '87 300D Sportline suspension, '79 300TD w/ 617.952 engine at 367,750 and counting!