OK, good to know you understand how EEPROM fits into things.

Trying to reduce the value of 100 for Z in DEFAULT_MAX_ACCELERATION is the only idea I have. This is again based on your observation that a single manual move of 10 or 20 mm measures out right. A manual move like that would only involve one acceleration and deceleration on Z, while a print would require acceleration/deceleration on every layer height adjustment. You might not notice a few missing steps on a single 10 or 20mm move, but the error would add up if that same number of missing steps occurs every layer shift.

I think there have been a few reports of the M5 threaded rods and nuts on MakerFarm i3v printers wearing out after a lot of use, especially on printers with automatic bed compensation. I don't recall whether the symptoms involved print height issues, but it's something to consider.

If you haven't already, I'd pull the threaded rods out or otherwise unconnect them from the x-carriage and make sure the x-carriage slides up and down smoothly and consistently.

Good luck.