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If the engine that was swapped in is really from a 2011 car, that is going to be a problem. A 2011 engine isn't a direct interchage with a 2006. I hope the car was a good deal becasue the only way this would probably work is to get factory service manuals for both years and check to see what is different.

You may be time and money ahead to sell the 2011 engine and get one that is compatible with the 2006 car which would generally be from a 2006-2008 car.
Electronics are different after 2007 or 2008, the 2011 computer won't work with the car's 2006 electronics.
 

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The 2011 PCM won't work with the 2006 car because it won't communicate with the other models. There is no way around that.
 
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