4.2/3.9 utilize the same, yes the same intake setup, the only difference is the stroke of the engines, 3.8/3.9 are the same, and yes the 3.9 was delveloped for freestar, but it is a tranverse mounted engine in freestar, the intake is rotated 180 drgrees verses the 4.2. I designed fuel rails for each, the 05 4.2, and the 06 3.9, so to put holes in the one year theory, the 3.9 will be introduced in 05 with the exsisting fuel rail that is on the 3.8 currently, then the new one will go one 06 with a commitment of at least 3 years worth of production. the talk of the 4.0 going in the stang has been around since 01, I personally would look for a 3.5 to be the next mustang base engine, not fact just rumored
the only thing I am aware of on the 3.9 to 4.2 that may be different are the cams, the head and intake combo are the same, and the only reason I say the cam is different is because truck engines are normally set up for lower end touque
on another note the 4.6 3v heads are different then the 5.4 3v heads. currently the 4.6 3v is the best of the 3 engines available in 3v configurations (4.6,5.4,6.8) ther 5.4 and 6.8 are being developed by the truck group, with the 4.6 being developed by the car side