Z axis error woes

[Jonathan]

it could be noise making the z step randomly

I just plotted the point list:



That doesn't look very random! In fact that's an excellent linear correlation (R²=0.9996) so it looks like an alignment problem to me. If you hadn't said that the bed was surfaced I would say that it is the gantry that's not level and if you hadn't said that the cut with a V-cutter looked fine I'd say it was the bed/PCB that's not level as a straight line like that implies one or the other is inclined.

One way to test if it's a cumulative error, for instance missing a couple of steps for every down move (seems unlikely but you never know), is to just do two points. One at Y0 and one at Y10 and see if the error is a 50th of what you just got from measuring 50 points.

This is why I sent you the 1mm endmill - with that the bed can be a lot further from level as the width of the cut does not depend on the height. Only problem is 1mm it a bit useless for anything but the simplest PCBs. I bought them on eBay as the seller said they were 0.5mm, but they weren't hence I've got no use for them.