Have you got a straight edge you can test the flatness of that flange with, and the flange on the manifold? Nuts need to be tight, but not monkey tight, or the aluminium can distort. ( but you know that)
Although not 180 degrees out, you can get it wrong so it fires on no.3 when you want it to fire on no.1, but I think you’re capable of overcoming that problem if it arises !