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They're pretty much the same. The 3.9 is just a stroked 3.8, if anything the 3.9 might have minimal amounts of torque greater than the 3.8, but it's very minimal. They're pretty even.
Yes, thinking about having an engine also used in a minivan brings up all kinds of negatives. Just remember though that the PCM and the remainder of the drivetrain used in the Mustang is completely different, and a 3.9L is a very good performer when used in a Mustang with the normal mods (dual exhaust, CAI, gears, flash tune). Try putting those on a minvan....