Is it just me or does that look like the op's car is a PZEV model? I see that there is a catalyst in the location aft of the one integrated into manifold but upstream of the muffler which is where they cut off the o.e. piping.
Here is what the ford parts catalog says the exhaust layout should be for a PZEV model.
Here is an image of what the car should look like O.E. without the second catalyst.