To report back:
It works now. I honestly have no idea why it didn't at first, the only explanation I have is that the first times I tried, when homing, the limit switch didn't trigger, which caused the Z-axis to refuse moving (this seems to be a safety setting in the firmware).
After coming back home yesterday and doing some more adjustments, the printer now prints fine in Cura as well as Slic3r, and I'll be replacing the endstop switch just to be on the safe side.
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DivingDuck 95
There is a plugin called Printer Settings on market place. I'm not quite sure wether this can help you, but there is a entry for "Z Endstop in Positive Direction". Check with care when you make adjustments with this plugin
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