It can be done, however they are not the same engine. The 2006 is a 4L and is a good bit different than the 3.8 you currently have.
You would need to do a lot to your car to make it work. The 2006 is also a drive by wire, not a drive by cable. So, you'd have to mess around with your gas pedal configuration as well, or make some sort of mechanical throttle body deal to work with the motor.
In short, I'd look for another V6 motor.
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Official Mustang Evolution Lake George Meet 2009

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