2nd layer issues and other
When I first assembled my Prusa last month I guess I was lucky, using the wizard I was then able to print without issues.
I moved the Mk3S into an enclosure, it's still open so heat isn't an issue. So I decided to start over with the wizard {including adjusting the PINDA}. Since then everything is a mess. I've readjusted the first level many times, bringing the Z level down.
First, with the Prusa ID plate the first level looked great but the second level was a mess. I finally successfully had a decent print then tried the Beer opener about 5 times with small adjustments to the Z level, still, I have issues with the 2nd layer.
Last night I tried the tug boat but as you can see the inlay on the front of the boat is a mess.
Placing the printer in its enclosure, a 15U server rack on a counter I leveled the plate before running the wizard. I don't know what else to do besides starting over again with the wizard.
RE: 2nd layer issues and other
I had similar issue that were caused by the Bondtech gears in the extruder becoming dirty or just not gripping the filament as it should.
As a result, it would miss layer lines, much like yours, primarily on infill! I think this is due to faster print speeds and higher extrusion rates while laying down the infill.
Try opening up the Bondtech gears, blowing them out with some computer duster, re-installing the filament, the load the filament. As the filament loads take a look and make sure the Bondtech gears aren't slipping on the filament while loading.
Rich 3D
https://3dnewb.com
RE: 2nd layer issues and other
Check your filament is coming in to the bondtech gear properly, also check the grub screw is on the extruder motor properly, if it slips then it will skip and not feed consistently.