You thread both pieces of the nut onto the lead screw in the same order they came off, with the slot in alignment. If the whole affair is put back in just like it came off, the nut will be no longer or any differently aligned than when the nut was still one piece. You do not screw them together until they touch. You leave the small gap that would have been there before you sliced it through and use the adjustment screw to pinch the two halves together to adjust out the backlash.
I find it easierst to install both nut halves on the lead screw and then slip the lead screw with the nut halves attached and lined up (key way), back into the bore they came out of the same way they came out. The backlash is adjusted minimal then by use of the adjusting screw you would have had to have removed to get the nut out in the first place. Since the back half of the nut is captured in place by a ridge and the adjusting screw squeezes the two halves together, you have the ability to adjust out the runout.
As previously mentioned, I think the manual recommends .005 as nominal. Zero runout is almost sure to accelerate wear.