JFTR, I just spotted a small discrepancy between the photos and the drawing of the (old) middle array.
Next to <http://www.vicious1.com/wp-content/uploads/2015/07/IMG_20150719_1230131.jpg>, you say, ‘Both Heads Facing up.’, consistent with the photos.
In the drawing in <http://www.vicious1.com/wp-content/uploads/2015/07/middle.png>, one bolt is shown head up, the other with its head on the bottom side. Probably functionally equivalent.
Is there any trick of loosening and re-fastening the parts of the middle section to maybe get rid of that misfit thread position? Of course, I could grind off some material of the bolt heads, but will the z-stepper drive assembly still fit and match?
You say there should be 2mm clearance between the M8 rod and the bolt heads next to the nut lock? No way here. I must have introduced a systematic error when assembling the parts. But where and what?