Ford won't have a clue. Or, more specifically, the people at Ford who do have a clue don't deal with the general public.
I'm pretty sure the 2.5L harness will work on the 3.0L engine, from what I understand, all of the sensors are in the same general location. Some sensors need to be changed (knock sensor I think, among others) because the ones on the 3.0L will have different connectors, and will not plug into the 2.5L harness.
I can tell you right now that the 3.0L engine harness will NOT plug into the computer harness on a Contour--the connectors are different.