So the wife bought a new van/box truck, 1997 e350. It has a v10 in it. The engine light came on and the code came back that it was an issue with the EGR valve. So I started looking around and found this opening. It looks like the, correct me if I am wrong the wording, air manifold is not made for this engine. Like some one swapped it out and didn't put the right one on it. You can see a hole open to the inside of the engine.

 

It could be you are getting an EGR code because there doesn't appear to be one there where it should be. Your assumption is probably correct. It's unbelievable what some people can do with parts, ie, "parts is parts". A lot will depend on the condition of the rest of the vehicle and if it has to pass any kind of inspection. It should be corrected.