Are your last 2 measurements down at the lower edges of the manifold flange, and are the first 4 measurements further up? If so, that thing has a good twist in it. Thicker gaskets might be a help in that.
BTW, did the block have the head locating pins in place, and were they snug/tight to the holes in the heads? My son and I made sure the heads were held down against the pins front and rear on both sides to align the heads the same (at least as good as the block machining was) while initially torquing the heads bolts. (Same setup as yours with new Edelbrock pieces.) That gave just a few thousandths manifold gap difference along all corners. Of course, it may just be the luck of the draw on manifold castings....
