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Unfortunately, when a car is totaled, the party that is at fault is only at fault for the value of the vehicle and any other damages like personal injury and medical bills. They can't be held responsible for the money you spent on repairs. Likewise, they can't be held responsible because you can't find an equivalent car at the replacement cost. The book value indicates that your car is as reliable and trustworthy as any other $5000 car. While your vehicle may have been especially well taken care of... the book value is all a court has to determine the value of a vehicle.
That said, the company is at fault and they or their insurance company should pay, not yours. You will have to bear increased cost to your insurance as a result and you have less room for argument about the true book value (there is more than one book, with more than one value).