I've recently discovered that the bolt holes on my upper plenum or off center enough to cause the ports to mismatch by quite a bit. It looks like Nissan took the casting and fixed it to the 8 hole drilling rig slightly rotated so that the front is aligned right but the rear is shifted over by a bout 2mm. So the rear two bolt holes are the most off center and the front two are almost perfect.
I could probably take it to a machine shop and have them fill all the off center holes with molten aluminum and then redrill, but I'm certain I can find a used plenum for much cheaper than that.