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Your '04 has the later, upgraded 3.8L with different heads.
in 2004 there were two V6's offered for the Mustang. One was the 3.8 and the other a 3.9. They are really very similar but the 3.9 had a slightly longer stroke. The power difference is neglible. Someone who used to work for Ford told me that the change was because they had a supply of 3.9's for the windstars and decided to use up the 3.8's and then if needed for a mid-year production use the 3.9's.

Mine had a 3.9. It had 401,000 miles on it when I sold it. I was pretty impressed with it given that my expectations for it were pretty low. I mean, after all, it did make more power than some of the fox body V8's did, and got 27mpg to boot. More toward 30 if you drove it right. I hated the sound of the engine as I hate the sound of any V6. The best exhaust for any V6 is a quiet one. Rotary muffler sure helps too.
 
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