Hmm...you've got an SVT, so if you've got the SVT throttle body gasket (sounds like what you described), then maybe you just need to flip it around a time or two to get it lined up right with the UIM. When I did my intake manifolds, I got the SVT TB gasket by mistake (I have a '97SE), but even after I got the proper one, I installed it upside down at first.

"Think of it, if you like, as a librarian with a G-string under the tweed." Clarkson on the Mondeo.