Hi - I’ve been setting Z manually off my stock for rotary projects and in Vcarve making that the Z as well. However, in my rounding toolpath job where I want to round a square piece of stock, I now want to set the Z to the center of the chuck from the initial calibration. Currently it’s Z’d at my previous job. I know I can manually drive it to the center of the chuck in the Set Part Zeroes, but I would rather have it exact. 
Is this Mach or EX? If EX it does that for you when you do the initial calibration: https://youtu.be/aKjV7_DNeyQ
What I do is remount that rod with the plastic sleeve that you used to calibrate it, and you can probe it from both sides (remembering to rotate the chuck 180 degrees between measurements, in case the rod isn’t perfect). Average the two positions, and you have the center, and know the “radius” of the rod at that point. You can probe the top to set the Z center too.
You can check for centered by putting a dowel or something in the chuck, and “making it square” in three places, once by cutting on the left four times, once by cutting on the right four times, and once by cutting on the top four times. If all three squares measure the same, you’re good. If not, you know how much you’re off by.
Why do I do it this way? I removed the chuck at one point, thinking it would go back on in the same place, and it didn’t… which meant relying on calibration and having the touch block on the tailstock didn’t work 
Live and learn! I got paranoid and spent an afternoon fixing it and then proving it was fixed.
Thanks Eric - got it sorted out!
Great tips - learning quite a bit with this thing! Thank you.