Skipped layers

[printbus]

Moisture in the filament leads to steam bubbles that pop from the nozzle, often resulting in small bumps or zits in the print.

Re-reading the thread, I don't follow the height error you describe in post 1. The gcode snippet starts at a height of 3.65mm. A z-hop up of 0.75mm for moving to the next layer gets you to 4.40mm. The move to the starting location for the new printing layer includes moving Z back to 3.75mm, which would be the original 3.65mm height + 0.75mm z-hop hop - 0.75mm z-hop down + 0.1mm for the new layer height. How is 3.75mm the incorrect z-height for the new layer?

A new thought - PLA can tend to curl up at corners and edges - especially if the temp is a bit high or you're over-extruding. At your through-holes, perhaps this leaves a slight ridge that catches the nozzle on subsequent passes. This catching could cause a mechanical twitch throughout your x-carriage and extruder that leaves the nozzle a bit out of place until additional movement lets things settle back into place. Your 0.1mm layer height would be more susceptible to this than say a layer height of 0.2mm. Adding an effective print cooling scheme is very helpful in improving PLA print quality, and might be part of the solution you are looking for.