I have a theory on this one. When the upper manifold is removed...I believe you will find the EGR stovepipe will not be in the lower intake manifold seated properly as it should be.
This missing stovepipe might be lodged in the upper manifold or was suppsed to have been replaced with a smaller diameter that came in the new manifold kit and someone forgot to put it back in.
I saw one case where a manifold was replaced, and unknowingly to myself and the person the pipe was missing. Bob Dillon then received the core manifold back and asked why we sent a sleeved one back. The base of the manifold gets erroded quickly when the hot exhaust gases beat on it directly. This can cause a premature failure by superheating the base of the composite manifold.
Please let us know about the stovepipe. It SHOULD be firmly in the lower intake manifold.
Here is our reassembly picture. Stovepipe is not there.