Those are the thermactor or AIR pump ports. The EGR ports are the ports in the middle of the intake side surface, between the two center bolts for the intake.
What Joel said. The passages at the back of the heads are for the thermactor and smog system. The EGR ports are between the two center intake bolt holes on the head. Some are round like the ones in the above pic. Most of the ones I have seen on the Ford production heads look like a small intake port.
You could potentially have an exhaust leak if you've got bits and pieces of your thermactor system torn apart. Make sure the ports on the back off your heads are plugged and same for the small tube on the midpipe if you don't have to worry about emmissions.