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No one has yet reported a problem with reduced diameter stovepipes restricting flow in the EGR system. More likely, the EGR valve is plugged up and needs a good cleaning. Another thing that can happen after LIM work is the corrugated stainless tube carrying exhaust gas from the EGR to the LIM can crack and leak, but it doesn't seem like that should cause a restricted flow code to set.
Was the EGR passage in the LIM clear before you drove in the new stovepipe?