Correcting for spindle runout

[Doddy]

Those spindles are good, but fairly heavy. You'll find the twin unsupported rails bowing under the weight mid-axis, resulting in the cutter gouging deeper into the PCB substrate. Same for the other axis. You can try to counter by Z-mapping the bed but it's a faff. For such a small machine I'd look at the 800W (smallest/lightest) spindle - but even that will have similar problems. As above, be realistic.

Edit: Measure your backlash as well - that could be similarly limiting.