They already have a 5 speed that mates to the 5.4 . . . in the Super Duty's

If I'm not mistaken, you can get a manual with the V10 and Diesel's as well. So the tranny is there just not in the light duty 5.4's.
That being said, it probably comes down to marketing and the fact that the vast majority of the 5.4's would be sold with the auto tranny even if the manual were available . . . I could be wrong, but I think most users would opt for the auto especially seing as how the truck market has gone "mainstream".
With the introduction of the new baby diesel in the light duty F-series, it will be interesting to see if a manual is an option . . .