The 3.9L motor was a special edition for the 2004 model year.And yes,the 3.9 is a slightly different motor.More specifically,it's a 3.9L Windsor.Th3 3.8's were not Windsor motors.I had an argument with one of the tech's at work several months back on this.There is no physical difference in the block between the two.But because it comes from a different manufacture,they rounded the number off more precisely. 3.8's are actually 3.89L but Ford just called it a 3.8. "Some" parts under the hood are different but most everything is the same.The PCM programming may be different but I'm not sure on specifics.