The flats of the shaft were at roughly 6 and 12, due to space constraints I'm not sure I can say with certainty they were exact. Before alignment I centered and locked the box and confirmed the wheel itself was perfectly centered and it was. After alignment all is well and signals cancel correctly.

The box I purchased didn't come with a pitman arm which I had to swap from my old box, the position of the pitman must have been slightly off from old to new just enough to throw the toe out of whack.