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There is another important module in the car which needs to be checked on this car for check engine lights. It's called the "Diagnostic Module". There MAY be codes in this module even if none are stored in the engine control module itself.
There is a bit of a known problem with these era engines for bad wiring harnesses. You should have codes in the engine control module if that was the case here though. Have them read out fault codes in the diagnostic module first.