my 6040 cnc runs mach 3    Design is done in fusion 360  G code exported with Mach3 mill plug in  Everything  seems fine except depth of cut especially with deep pockets(not deep enough cut, sometimes off by as much as 5mm!!)   It may have nothing to do with anything I mentioned   I may be setting z zero incorrectly   at the moment I jog down to get the tip of the tool to touch the top of the stock and then zero the z axis  what is a good and reliable way to get z zero? any other reasons or suggestions re the depth of cut problem?

Z axis calibration? (steps per)

Some further info on this problem
I checked the actual distance traveled against the digital readout   x and y axes are perfect as the distance coincides with the readout    the z axis as an example shows a readout of 29 while the actual travel is only 21 or 22 does this mean that the motor is missing steps, say one in every 4   readout  28/29 versus travel 21/22   roughly the travel is 3/4 of the readout
any advice would be highly appreciated

As ZASto has already said - check your 'Z axis calibration? (steps per)'

The Mach3 Settings page has an Axis Calibration Set Steps per Unit - just click and follow the on-screen instructions to check your Z axis steps per are correct.

Tweakie.