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I'm pretty sure you misread the code. P0039 is a DTC related to a turbo problem. This car does not have a turbo.

P0339 is a crankshaft position sensor issue. This is a serious issue, as without an accurate CPS signal, the engine will not start or run. Your engine presently has an unstable/irregular signal going to the cars computer. This is not something to screw around with. You either have a failing CPS, or damaged wiring harness.

As to your question re seam discoloration. Impossible to say without seeing it. If it is rust colored, you are in trouble as the panels seams are rusting badly. This could be a result of the car getting submerged in a flood, or having a careless owner who did not wash the car in a salty location.

I'd be concerned about a flood history as this would also explain the CPS fault.
 
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