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I am seeing an issue on my prints in some places that almost seems like over-extrusion. This is happening in some area's, and on this print it is when the printer starts extruding after (what I am assuming is) a retraction. I am attaching a picture of the print, along with the gcode. This was sliced with Simplify3D.

That artifact is pretty typical if you print anything with a hole in a vertical face you'll probably see what appears to be slight misalignment for the duration of the hole.
What I believe that is, is slight backlash, the head moves differently when the hole is present and the difference in motion coupled with the slight backlash causes a tiny layer shift.
Now tracking it down and fixing it is a somewhat harder problem, your looking for any even slight slop in the motion.