Losing steps and calibration

I have spent almost the whole week recalibration and fine tuning the machine and have finally tried a project. Unfortunately it seems like it is now missing a step, I was cutting a box and noticed it seemed like the joints were getting smaller so I stoped it and realized there was a ridge like it had shifted.

My main question is will I have to recalibrate the $100 & $101 after I adjust the pots?

Also does anyone have a better way to set the pots I did it when I first got it and it was quite tedious and not very precise.

Yeah pots, sorry I could have sworn they were poles. Fixed it.

Thanks, this is actually the process I used the first time round, and what I did this morning, I was just sort of hoping there was a more exact method. I am just a little dubious of the trial and error method on a thousand dollar piece of equipment.