I am building a Prusa i3 MK2 Clone and I am caught on this one. I have replaced the extruder with a MK8 adapted by myself to fit with most of the previous hardware from the E3D style extruder.
My current problem is that the nozzle appears to be dragging on the top of the layers. I can't tell if it's over extrusion or a layer height issue or what. I am testing by printing the 20mm calibration cube. The dimensions appear to be spot-on, but the layers start building up too much filament such that it just gets re-melted and shuffled around:
Anyone have a clue what this could be? Software, Hardware, Slic3r Settings?
I have: 0.5mm Nozzle Diameter. MK8 Direct Drive extruder.
Anything else you want to know?
--- UPDATE ---
Thanks everyone for your help. Turns out it was seriously over-extruding, like 3x what it should have been! I ran through this instructable: http://www.instructables.com/id/How-to-calibrate-the-Extruder-on-your-3d-Printer/ Which helped me with what I needed to do to fix the issue, but just re-flashed Marlin on the printer with the updated setting.
Here's the result! WAY better, I still have some z-wobbling issues but i think the frame just needs more support than it has now and that should fix up the slightly jagged corners.
You stated your print of a 20mm cube came out spot on so I will rule out any z-axis configuration issues. It clearly seems like you are extruding too much plastic.
I use slic3r myself with repetier so I am familiar with the settings.
Print Settings - Advanced
All the values should be 0 except first layer sometimes is 100%-200% depending on your personal setup. Increasing these values may cause more filament to leave the extruder.
Filament Settings - Diameter
This should be set to 1.75 or 3 depending on your filament size. If you accidentally have it set to 1.75 when your filament is 3mm, it would probably be over-extruding since it pushing almost double the plastic with the same length.
Filament Settings - Extrusion multiplier
This should be set to 1 or slowly adjust it 0.05 increments to reduce overall amount of plastic leaving the nozzle.
Printer Settings - Nozzle diameter
This should be set to 0.5 since your nozzle is 0.5mm. Make sure your nozzle truly is this value.
EDITED 10/19/17 - OP has solved problem and his own answer made me realize I made mistake on how to measure and correct extrusion steps/mm. Ignore this below and see what OP wrote in their edit.
If all these Slic3r configurations fail or are correct and do not solve your problem, I think you may want to look into your motor step settings for the extruder. It may be too high pushing more filament than it should. To correct this, you need to do the length test where you will extrude 10mm or 50mm and measure the string of plastic. There might be some stretch so a 10mm may measure as 11mm but as long as your close it should be good. If you extrude 10mm and you measure 25mm, you need to recalculate your steps per mm.
Also for your first layer, make sure it is not being smushed to the build plate. You want it to be flattened a little to provide good adhesion but not too close to the build plate where it would constrict the nozzle.
Hope this helps, and good luck on your prints. May you never have to deal with thermal runaway error :)