I suspect that this interference issue may be caused by a combination of two issues. Warpage of the flange on the pipe, during the welding operation. Distortion of the exhaust port due to either/or/both prior overheating of the cylinder head, causing the exhaust ports [hottest section of the head] to warp. Over tightening of the exhaust retaining nuts by the previous owner(s).
I wonder if the difference in circumference of the flanges of the old versus new pipes is actually a manufacturing defect, or simply wear on the flange of the old pipe? Is the chrome plating still intact on the circumference of the old pipe flange?