Nozzle Diameter Affects Print Quality

I built my printer and so I did not have the benefit of a factory calibration, however I have learned a great deal about printer settings and the various outcomes.  At first the nozzle diameter setting in Slic3r seemed to be plug and play.  The nozzle I purchased says it's a .40 so that is what I put into Slic3r.  Consequently my prints were coming out awful because over time the nozzle was getting farther and farther away from the item.  The distance is incredibly small but matter greatly.

The issue is that what Slic3r thinks it is extruding out of your nozzle does not equal reality.  Depending on the actual size of your nozzle and the setting you put in, it might be putting out a lot less or a lot more than it thinks it is.  With my first nozzle labeled as a .40, which is what I put into slic3r was closer to 0.38.  This is a such a small discrepancy but it matter because my exterior layers were showing gaps and not properly laying on top of each other.  In this case Slic3r thinks it is putting out .40 worth of material and compensating appropriately on the Z-axis for each layer.

My next nozzle was just the opposite, and I was getting squashed wide extrusion lines.  My layers no longer had gaps but my prints were shorter and wider than they should have been.

The fastest way to calibrate this is to do a small area but tall print and make small adjustments to the nozzle diameter.  Keep in mind that this setting goes hand in hand with the filament diameter.  Hopefully you have digital calipers (I bought mine from Amazon) to verify the width of your filament, and would also be useful in verifying the dimensions of your printed object.

In your settings...
Nozzle diameter to large, will result in gaps between layers.
Nozzle diameter to small, will result in smashed wide strands.

Both issues will get worse as your print height goes up.

The Bad

Examples of when my nozzle was set to large than it actually was.  Gaps occurred because the filament did not land right on top of the previous layer.

The Good

Once you get the nozzle amount dialed in the lines come out very clean.  I believe I printed this at 200 microns.