SOURCE: getting diagnostic error code 1004
P1004 - SHORT RUNNER VALVE CONTROL PERFORMANCE
P1004 is for the performance of the intake plenum's short runner valve actuator. This is an electrical actuator on the intake that opens and closes a valve in the plenum under certain driving conditions to provide better performance.
There was a service bulletin for this code and is the first thing that needs to be done. Your dealer may have already done this, or is in the process of completing it with the repair you were quoted. The TSB involves reprogramming the software in the powertrain control module and then checking to see if the short runner valve actuator works correctly. After the software is updated then the actuator is commanded to sweep using the scan tool. If it doesn't sweep correctly then the actuator is removed and the valve is moved by hand. If any binding in the valve is felt then the intake plenum has to be replaced. If no binding is felt and the wiring to the actuator is intact, then the actuator will need to be replaced.
It sounds from your description that this is what the dealer is doing. I would say that the software has been updated and they found that the short runner valve was binding, and the plenum needs to be replaced. It wouldn't cost $2,000 though. The plenum itself runs $449 and the labor to replace it shouldn't exceed two hours.
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