I have a set of 243 heads and the first intake valve I pulled out I saw that the intake valve seat protruded into the intake port on the long radius side. The port is larger than the seat inside diameter making a step where the seat ring is. Is this common or should I look for another set of heads?

 

very common on stock castings. Take a grinder with some carbide bits and blend it into the bowl if your not liking the way it looks.