The engine harness isn't what plugs into the ECU. The computer/power harness is what plugs into the ECU.
Look at your Duratec V6 engine. See the several plugs on the passenger's side of the engine, near the engine mount? Those are what join the engine harness with the computer/power harness. Those plugs are unique to the Contour.
Now I suppose if you were willing you could chop them off your existing engine harness and splice 'em to the 3.0L engine harness....
