Install rear take down pin, leave front take down pin out, push upper tight against lower and take a photo of the through channels for both to post so we can see just how far they are off.
Hence tight to get the pins to lock up to start with on new parts, self solves it own problems as the pin will just slightly enlarge the needed channel via live fire. So lock up channels being off by a few hundreds of thousands, not the end of the world.
On the other hand, fail to allow the channels/pins to mate up, could end up with a sloppy mess in the end.