5.4

in a past issue of 5.0 Mustang and Super Fords they have a white Boss (yes I said Boss and YES its a Ford made one, not Shinoda (thought they may have been invloved) its a SVT project) with a V10 in it, in the article they couldnt figure out how to get the clutch to hold the power, even the SVT clutch off the cobra was failing on them.
 
the 4.6 was a better option becuase its powerband was in the right location for a mustang. the 4.6 can rev higher than the 5.4 (in stock forms) and thats generally what the mustang owner wants. also i dont think ford had an aluminum 5.4 in 96 so the cobra wouldnt have worked. plus they needed to have the 4.6 in something besides the crown vic/grand marquis/town car and the thunderbird/cougar/mark8.
 
I thought the "R" was more Like 80K, but the reason it cost so much was the quality of the parts. It had forged everything on the engine side, and after market everything on the suspension side. Putting a "normal" 5.4 into a mustang shouldnt cost Ford anymore than putting a 4.6 into a mustang (as far as parts go). I think the problem is more along the lines of getting the car emissions certified by the government. If Ford put the 5.4 in all GT's and didnt have low enough emissions the government would levy a pretty hefty terrif against ford. So, I guess in that respect it is a cost issue. For all I know this is why LS1 camaros cost a few thousand more than the stang.