What we need is a better method that does not rely so much on machine calibration. If the depth is a problem one must use a shim for the touch or adjust the depths of the mpc. If it is line up of the front to back, let me suggest another technique. The pipe mpc here is split into two files. One for the back and one for the front. The one for the back has a center hole drilled in it (You will have to load the 1/8 cutting bit just for the hole.) After the back is carved, flip it over and choose jog to position instead of center on board. When you get to jog to edge or center, pick jog to center. Jog to the hole so that by pushing the truck down, you can push the bit into the hole. The y will line up automatically since the truck will move manually. It is the x that requires some effort since you have to use the arrow keys. Now away you go. You cannot get much better than that for line up I do not think. The method should be independent of the machine calibration. I have planned to experiment more with this method but have not gotten to it.
Don't give up. Hell I will send you a pipe if you cannot carve one.