Z-axis Calibration / Cutting Too Deep

Between projects, I’m still working on the fine tuning/calibration aspect of my machine. I think I understand the impact that belt tension and v-wheel tension have on the accuracy of the X and Y axis, and that these components need to be checked and adjusted as required on a regular basis. I have to confess that I’m not sure if belts (or v-wheels, for that matter) that are either too loose or too tight cause the machine to either overcut or undercut a design element, so I would appreciate any insight anyone has in that regard. But the calibration process is fairly straight forward and easy to perform on a periodic basis.
But calibrating my Z-axis and getting accurate results is proving more elusive. After getting some advice as to the default value and starting point of $102 last week, I set up a calibration process using a 1-2-3 block, a set Veritas setup bars and a set of feeler gauges. Long story short, I jogged the machine up 2.25" and measured the results…actual machine travel was about 0.0015 greater, so I made the necessary adjustment to $102.
I then stole an idea from one of @HaldorLonningdal’s posts and cut a shallow pocket, 8" square with a 1" surfacing bit to a depth of 1/32". The surface results of that operation were much better than I expected…no ridges in either direction, so I’m reasonably satisfied that my Z-axis is perpendicular to both the X and Y axis. BUT, it was machined about 0.007/0.008" too deep, and fairly constant at all four corners. But as I was using MDF, that may be a result of material thickness differences. I then machined a second smaller pocket inside the first with a 0.25" end mill and re-setting Z-zero using a Tri-Quetra touch plate on the bottom surface of the first pocket to a depth of 0.25". The results were better, but the cut was still about 0.0055" too deep. Again, fairly constant at all four corners.
I guess I’m looking for confirmation as to whether my Z-axis calibration process is reasonable, and whether my results are within an acceptable tolerance for a 750 mm X-Carve. I’m thinking of repeating the process using something other than MDF which I can run through my planer to yield a more constant thickness.

I think you are headed in the right direction. I think you tolence is close but i guess it depends on what you are cutting and how close you need it. Also running a board thru a planner will not flatten it it will take it to a desired thickness. If yoy want to flatten it you need to run it over a jointer first and get 1 true flat side then work with the planner.

You are correct in so far as using a jointer before the planing process! Thanks for pointing that out.
I do have a 6" jointer and 13" planer, so maybe I’ll prepare enough material so I can run the calibration process, but with smaller pockets, and at all four corners as well as the center of my machine. I can then compare the results.

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