In addition to some other issues, the latest thing is this inconsistency in Z height
Any guidance would be appreciatedYou might double check that your z-axis carriage is square to your work surface, I believe I saw someone else on here that was seeing a similar effect and that cleared it up for him. You might also try a small test pocket with another endmill to see if it’s a problem with the tool. Make sure that the bit is as far into the collet as it can go (without covering up any of the cutting surface).
When I put my machine together for the first time, my Z-Axis lead screw nylock nut wasn’t tightened down all the way and this gave some play in the z-axis causing similar isuues.
There’s also the usual stuff to check like belt tension and v-wheels.