No, the SHO motors were mass produced. However they do have very tight tolerances for a mass production engine, this is part of the reason they last so long I believe.
The SVT engines in the Cobra are hand assembled by two assembly men. They sign the valve cover, neither of the signatures/initals are john colletti's tho.
I'm not sure if the other SVT engines are signed, I'm pretty sure they aren't. Oh, and the SVT contour engine wasn't hand assembled, so I doubt the Focus and Lightning engines are too.
-Martin