Anything less than 97% extrusion results in visible gaps on the top layers
One other thought, since your hot end mount is 3d printed, check to make sure it’s not wobbling.
If your extrusion is ok and the filament is ok, that kind of print surface issue is most likely caused by XY looseness. Bed shifting, groovemount loose, belt backlash, etc.
Z rod wobble (bent screw)?
anu apa sih
i have had this same problem 3 times now, one of them deliberate…
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if you are using slic3r prusa edition, try to reduce the number of perimeters. there’s a bug (still unsolved) i can demonstrate where (especially on round objects), the perimeters are not calculated properly and it looks exactly like that. i have no idea if this happens in regular slic3r as well since i have not tried it.
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backlash - from one of your belts being on too tight (could also be too loose). if you look closely at your pictures - it looks like this happens to one side more than others. if the first picture is indicative of the orientation it was printed - then it looks like it is the y axis.
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i caused this on purpose in order to settle an argument - why stiff couplers are (usually) a bad idea on diy 3d printers (and more specifically diy printers with parts printed by other diy 3d printers). theoretically, your setup (of an embedded leadscrew stepper motor) is the same, so, if there is any misalignment between your z rods and your z leadscrews it would cause the same effect.
this could be caused, e.g - by your 3d printed parts being printed on a printer with non-perpendicular x & y axes, which would cause a deviation between the part holding the z motor and the part holding the z axis and riding the leadscrews.
@NathanielStenzel i hope not. Lead screws are expensive lol